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.

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.

Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

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

Kamberaj, Hiqmet, E-mail: hkamberaj@ibu.edu.mk

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, andmore » 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.« less

Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2015-09-01

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

Development and validation of a canine radius replica for mechanical testing of orthopedic implants.

PubMed

Little, Jeffrey P; Horn, Timothy J; Marcellin-Little, Denis J; Harrysson, Ola L A; West, Harvey A

2012-01-01

To design and fabricate fiberglass-reinforced composite (FRC) replicas of a canine radius and compare their mechanical properties with those of radii from dog cadavers. Replicas based on 3 FRC formulations with 33%, 50%, or 60% short-length discontinuous fiberglass by weight (7 replicas/group) and 5 radii from large (> 30-kg) dog cadavers. Bones and FRC replicas underwent nondestructive mechanical testing including 4-point bending, axial loading, and torsion and destructive testing to failure during 4-point bending. Axial, internal and external torsional, and bending stiffnesses were calculated. Axial pullout loads for bone screws placed in the replicas and cadaveric radii were also assessed. Axial, internal and external torsional, and 4-point bending stiffnesses of FRC replicas increased significantly with increasing fiberglass content. The 4-point bending stiffness of 33% and 50% FRC replicas and axial and internal torsional stiffnesses of 33% FRC replicas were equivalent to the cadaveric bone stiffnesses. Ultimate 4-point bending loads did not differ significantly between FRC replicas and bones. Ultimate screw pullout loads did not differ significantly between 33% or 50% FRC replicas and bones. Mechanical property variability (coefficient of variation) of cadaveric radii was approximately 2 to 19 times that of FRC replicas, depending on loading protocols. Within the range of properties tested, FRC replicas had mechanical properties equivalent to and mechanical property variability less than those of radii from dog cadavers. Results indicated that FRC replicas may be a useful alternative to cadaveric bones for biomechanical testing of canine bone constructs.

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.

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.

Replica Exchange Improves Sampling in Low-Resolution Docking Stage of RosettaDock

PubMed Central

Zhang, Zhe; Lange, Oliver F.

2013-01-01

Many protein-protein docking protocols are based on a shotgun approach, in which thousands of independent random-start trajectories minimize the rigid-body degrees of freedom. Another strategy is enumerative sampling as used in ZDOCK. Here, we introduce an alternative strategy, ReplicaDock, using a small number of long trajectories of temperature replica exchange. We compare replica exchange sampling as low-resolution stage of RosettaDock with RosettaDock's original shotgun sampling as well as with ZDOCK. A benchmark of 30 complexes starting from structures of the unbound binding partners shows improved performance for ReplicaDock and ZDOCK when compared to shotgun sampling at equal or less computational expense. ReplicaDock and ZDOCK consistently reach lower energies and generate significantly more near-native conformations than shotgun sampling. Accordingly, they both improve typical metrics of prediction quality of complex structures after refinement. Additionally, the refined ReplicaDock ensembles reach significantly lower interface energies and many previously hidden features of the docking energy landscape become visible when ReplicaDock is applied. PMID:24009670

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.

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.

New dichromated gelatin technologies for diffraction optical element fabrication

NASA Astrophysics Data System (ADS)

Vigovsky, Yury N.; Malov, Alexander N.; Malov, Sergey N.; Feshchenko, Valeriy S.; Konop, Sergey P.

1998-01-01

The hologram recording mechanism in the dichromated gelatin layers are discussed. A new technologies are described for red rainbow hologram recording in the photographic emulsion and selfdeveloped dichromated gelatin--glycerol layers. A new method is suggested and experimentally approbated for relief plastic replica of the rainbow hologram fabrication based on the tanning developed or bleached photographic emulsion. This method is modification of the old photographic `bromoil' process. Some aspects of the noncoherent hologram coping on the dichromated gelatin films are discussed too.

Short fatigue crack behavior in notched 2024-T3 aluminum specimens

NASA Technical Reports Server (NTRS)

Lee, J. J.; Sharpe, W. N., Jr.

1986-01-01

Single-edge, semi-circular notched specimens of Al 2024-T3, 2.3 mm thick, were cyclicly loaded at R-ratios of 0.5, 0.0, -1.0, and -2.0. The notch roots were periodically inspected using a replica technique which duplicates the bore surface. The replicas were examined under an optical microscope to determine the initiation of very short cracks and to monitor the growth of short cracks ranging in length from a few tens of microns to the specimen thickness. In addition to short crack growth measurements, the crack opening displacement (COD) was measured for surface cracks as short as 0.035 mm and for through-thickness cracks using the Interferometric Strain/Displacement Gage (ISDG), a laser-based optical technique. The growth rates of short cracks were faster than the long crack growth rates for R-ratios of -1.0 and -2.0. No significant difference between short and long crack growth rates was observed for R = 0.0. Short cracks had slower growth rates than long cracks for R = 0.5. The crack opening stresses measured for short cracks were smaller than those predicted for large cracks, with little difference appearing for positive R-ratios and large differences noted for negative R-ratios.

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.

Hard- and software problems of spaced meteor observations by optical electronics

NASA Technical Reports Server (NTRS)

Shafiev, R. I.; Mukhamednazarov, S.; Ataev, A. SH.

1987-01-01

An optical electronic facility is being used for meteor observations along with meteor radars and astronomical TV. The main parts of the facility are cameras using UM-92 optical electronic image tubes. The three cascade optical electronic image tube with magnetic focusing has a 40 mm cathode and resolution in the center of up to 30 pairs of lines/mm. The photocathode is of a multislit S-20 type. For meteor spectra observations, replica gratings of 200 and 300 lines/mm are used as the dispersive element.

Accuracy and repeatability of long-bone replicas of small animals fabricated by use of low-end and high-end commercial three-dimensional printers.

PubMed

Cone, Jamie A; Martin, Thomas M; Marcellin-Little, Denis J; Harrysson, Ola L A; Griffith, Emily H

2017-08-01

OBJECTIVE To assess the repeatability and accuracy of polymer replicas of small, medium, and large long bones of small animals fabricated by use of 2 low-end and 2 high-end 3-D printers. SAMPLE Polymer replicas of a cat femur, dog radius, and dog tibia were fabricated in triplicate by use of each of four 3-D printing methods. PROCEDURES 3-D renderings of the 3 bones reconstructed from CT images were prepared, and length, width of the proximal aspect, and width of the distal aspect of each CT image were measured in triplicate. Polymer replicas were fabricated by use of a high-end system that relied on jetting of curable liquid photopolymer, a high-end system that relied on polymer extrusion, a triple-nozzle polymer extrusion low-end system, and a dual-nozzle polymer extrusion low-end system. Polymer replicas were scanned by use of a laser-based coordinate measurement machine. Length, width of the proximal aspect, and width of the distal aspect of the scans of replicas were measured and compared with measurements for the 3-D renderings. RESULTS 129 measurements were collected for 34 replicas (fabrication of 1 large long-bone replica was unsuccessful on each of the 2 low-end printers). Replicas were highly repeatable for all 3-D printers. The 3-D printers overestimated dimensions of large replicas by approximately 1%. CONCLUSIONS AND CLINICAL RELEVANCE Low-end and high-end 3-D printers fabricated CT-derived replicas of bones of small animals with high repeatability. Replicas were slightly larger than the original bones.

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.

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.

Study of Lightweight Ni-Co Alloy Mirrors Obtained by Electroforming Techniques

NASA Technical Reports Server (NTRS)

Jones, Ruth; Muntele, Iulia; Muntele, Claudiu; Zimmerman, Robert; Ila, Daryush; Smith, W. Scott (Technical Monitor)

2002-01-01

One contribution in reducing the costs of optics in space can be provided by production of ultralight mirrors. The decrease in the weight of the primary mirror of a telescope is anticipated to lead to the possibility of increasing the size of the telescopes, therefore increasing the amount and distance from which information is received. An electroplating process of ultralight replica mirrors from nickel sulfamate solution will be described. Based on an experimental setup with cylindrical symmetry, flat mirrors with a diameter of 7 inches and thickness of 1.5 mm are made from a Ni-Co alloy. The composition of the resulting deposit is analyzed using Rutherford Backscattering Spectrometry (RBS) and Proton Induced X-ray Emission (PIXE). In order to resolve Ni and Co, 10 MeV nitrogen ions are used as projectiles in the RBS measurements. Solution parameters monitored during the deposition process using optical absorption and polarography will be correlated with the final concentration of Ni and Co in the deposit. Bath parameters like temperature, current density, agitation level and acidity are chosen at certain values and maintained constant from one sample to another throughout the deposition process. The purpose of the experiment is to obtain mirrors with near zero stress, and predetermined composition and hardness. This study is an intermediate step in obtaining through the same process, but with a larger scale setup, ultralight large aperture replica mirrors.

Microstructural study of the nickel-base alloy WAZ-20 using qualitative and quantitative electron optical techniques

NASA Technical Reports Server (NTRS)

Young, S. G.

1973-01-01

The NASA nickel-base alloy WAZ-20 was analyzed by advanced metallographic techniques to qualitatively and quantitatively characterize its phases and stability. The as-cast alloy contained primary gamma-prime, a coarse gamma-gamma prime eutectic, a gamma-fine gamma prime matrix, and MC carbides. A specimen aged at 870 C for 1000 hours contained these same constituents and a few widely scattered high W particles. No detrimental phases (such as sigma or mu) were observed. Scanning electron microscope, light metallography, and replica electron microscope methods are compared. The value of quantitative electron microprobe techniques such as spot and area analysis is demonstrated.

Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing.

PubMed

Gallicchio, Emilio; Xia, Junchao; Flynn, William F; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M

2015-11-01

Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.

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.

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.

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.

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.

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.

Superconductor lunar telescopes --Abstract only

NASA Technical Reports Server (NTRS)

Chen, P. C.; Pitts, R.; Shore, S.; Oliversen, R.; Stolarik, J.; Segal, K.; Hojaji, H.

1994-01-01

We propose a new type of telescope designed specifically for the lunar environment of high vacuum and low temperature. Large area UV-Visible-IR telescope arrays can be built with ultra-light-weight replica optics. High T(sub c) superconductors provide support, steering, and positioning. Advantages of this approach are light-weight payload compatible with existing launch vehicles, configurable large area optical arrays, no excavation or heavy construction, and frictionless electronically controlled mechanisms. We have built a prototype and will be demonstarting some of its working characteristics.

Superconductor lunar telescopes --Abstract only

NASA Astrophysics Data System (ADS)

Chen, P. C.; Pitts, R.; Shore, S.; Oliversen, R.; Stolarik, J.; Segal, K.; Hojaji, H.

1994-06-01

We propose a new type of telescope designed specifically for the lunar environment of high vacuum and low temperature. Large area UV-Visible-IR telescope arrays can be built with ultra-light-weight replica optics. High Tc superconductors provide support, steering, and positioning. Advantages of this approach are light-weight payload compatible with existing launch vehicles, configurable large area optical arrays, no excavation or heavy construction, and frictionless electronically controlled mechanisms. We have built a prototype and will be demonstarting some of its working characteristics.

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.

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

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

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.

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.

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

Polarization chaos and random bit generation in nonlinear fiber optics induced by a time-delayed counter-propagating feedback loop.

PubMed

Morosi, J; Berti, N; Akrout, A; Picozzi, A; Guasoni, M; Fatome, J

2018-01-22

In this manuscript, we experimentally and numerically investigate the chaotic dynamics of the state-of-polarization in a nonlinear optical fiber due to the cross-interaction between an incident signal and its intense backward replica generated at the fiber-end through an amplified reflective delayed loop. Thanks to the cross-polarization interaction between the two-delayed counter-propagating waves, the output polarization exhibits fast temporal chaotic dynamics, which enable a powerful scrambling process with moving speeds up to 600-krad/s. The performance of this all-optical scrambler was then evaluated on a 10-Gbit/s On/Off Keying telecom signal achieving an error-free transmission. We also describe how these temporal and chaotic polarization fluctuations can be exploited as an all-optical random number generator. To this aim, a billion-bit sequence was experimentally generated and successfully confronted to the dieharder benchmarking statistic tools. Our experimental analysis are supported by numerical simulations based on the resolution of counter-propagating coupled nonlinear propagation equations that confirm the observed behaviors.

Full size Euclid grism prototype made by photolithography: first optical performance validation

NASA Astrophysics Data System (ADS)

Grange, R.; Caillat, A.; Pascal, S.; Ong, C.; Ellouzi, M.; Prieto, E.; Dohlen, K.

2017-11-01

The ESA Euclid mission is intended to explore the dark side of the Universe, particularly to understand the nature of the dark energy responsible of the accelerating expansion of the Universe. One of the two probes carried by this mission is the Baryonic Acoustic Oscillation (BAO) that requires the redshift measurements of millions of galaxies. In the Euclid design, these massive NIR spectroscopic measurements are based on slitless low resolution grisms. These grisms with low groove density and small blaze angle are difficult to manufacture by conventional replica process. Two years ago we started a CNES R&D program to develop grism manufacturing by the photolithographic process which is well adapted to coarse gratings. In addition, this original method allows introducing optical aberration correction by ruling curved and non-parallel grooves in order to simplify the instrument optical design. During the Euclid Phase A, we developed several prototypes of gratings made by photolithography. In this paper, we present the optical performance test results, including tests in the specific environment of the Euclid mission.

Consistency properties of chaotic systems driven by time-delayed feedback

NASA Astrophysics Data System (ADS)

Jüngling, T.; Soriano, M. C.; Oliver, N.; Porte, X.; Fischer, I.

2018-04-01

Consistency refers to the property of an externally driven dynamical system to respond in similar ways to similar inputs. In a delay system, the delayed feedback can be considered as an external drive to the undelayed subsystem. We analyze the degree of consistency in a generic chaotic system with delayed feedback by means of the auxiliary system approach. In this scheme an identical copy of the nonlinear node is driven by exactly the same signal as the original, allowing us to verify complete consistency via complete synchronization. In the past, the phenomenon of synchronization in delay-coupled chaotic systems has been widely studied using correlation functions. Here, we analytically derive relationships between characteristic signatures of the correlation functions in such systems and unequivocally relate them to the degree of consistency. The analytical framework is illustrated and supported by numerical calculations of the logistic map with delayed feedback for different replica configurations. We further apply the formalism to time series from an experiment based on a semiconductor laser with a double fiber-optical feedback loop. The experiment constitutes a high-quality replica scheme for studying consistency of the delay-driven laser and confirms the general theoretical results.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Nanoimprinting on optical fiber end faces for chemical sensing

NASA Astrophysics Data System (ADS)

Kostovski, G.; White, D. J.; Mitchell, A.; Austin, M. W.; Stoddart, P. R.

2008-04-01

Optical fiber surface-enhanced Raman scattering (SERS) sensors offer a potential solution to monitoring low chemical concentrations in-situ or in remote sensing scenarios. We demonstrate the use of nanoimprint lithography to fabricate SERS-compatible nanoarrays on the end faces of standard silica optical fibers. The antireflective nanostructure found on cicada wings was used as a convenient template for the nanoarray, as high sensitivity SERS substrates have previously been demonstrated on these surfaces. Coating the high fidelity replicas with silver creates a dense array of regular nanoscale plasmonic resonators. A monolayer of thiophenol was used as a low concentration analyte, from which strong Raman spectra were collected using both direct endface illumination and through-fiber interrogation. This unique combination of nanoscale replication with optical fibers demonstrates a high-resolution, low-cost approach to fabricating high-performance optical fiber chemical sensors.

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

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.

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.

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.

Phase stabilization of multidimensional amplification architectures for ultrashort pulses

NASA Astrophysics Data System (ADS)

Müller, M.; Kienel, M.; Klenke, A.; Eidam, T.; Limpert, J.; Tünnermann, A.

2015-03-01

The active phase stabilization of spatially and temporally combined ultrashort pulses is investigated theoretically and experimentally. Particularly, considering a combining scheme applying 2 amplifier channels and 4 divided-pulse replicas a bistable behavior is observed. The reason is mutual influence of the optical error signals that is intrinsic to temporal polarization beam combining. A successful mitigation strategy is proposed and is analyzed theoretically and experimentally.

Replica exchange with solute tempering: A method for sampling biological systems in explicit water

NASA Astrophysics Data System (ADS)

Liu, Pu; Kim, Byungchan; Friesner, Richard A.; Berne, B. J.

2005-09-01

An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST is compared with standard replica exchange for an alanine dipeptide molecule in water. The comparisons confirm that REST greatly reduces the number of CPUs required by regular replica exchange and increases the sampling efficiency. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water. Author contributions: B.J.B. designed research; P.L. and B.K. performed research; P.L. and B.K. analyzed data; and P.L., B.K., R.A.F., and B.J.B. wrote the paper.Abbreviations: REST, replica exchange with solute tempering; REM, replica exchange method; MD, molecular dynamics.*P.L. and B.K. contributed equally to this work.

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

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.

Broadband optical frequency comb generator based on driving N-cascaded modulators by Gaussian-shaped waveform

NASA Astrophysics Data System (ADS)

Hmood, Jassim K.; Harun, Sulaiman W.

2018-05-01

A new approach for realizing a wideband optical frequency comb (OFC) generator based on driving cascaded modulators by a Gaussian-shaped waveform, is proposed and numerically demonstrated. The setup includes N-cascaded MZMs, a single Gaussian-shaped waveform generator, and N-1 electrical time delayer. The first MZM is driven directly by a Gaussian-shaped waveform, while delayed replicas of the Gaussian-shaped waveform drive the other MZMs. An analytical model that describes the proposed OFC generator is provided to study the effect of number and chirp factor of cascaded MZM as well as pulse width on output spectrum. Optical frequency combs at frequency spacing of 1 GHz are generated by applying Gaussian-shaped waveform at pulse widths ranging from 200 to 400 ps. Our results reveal that, the number of comb lines is inversely proportional to the pulse width and directly proportional to both number and chirp factor of cascaded MZMs. At pulse width of 200 ps and chirp factor of 4, 67 frequency lines can be measured at output spectrum of two-cascaded MZMs setup. Whereas, increasing the number of cascaded stages to 3, 4, and 5, the optical spectra counts 89, 109 and 123 frequency lines; respectively. When the delay time is optimized, 61 comb lines can be achieved with power fluctuations of less than 1 dB for five-cascaded MZMs setup.

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

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

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.

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.

A Validation Study of the Impression Replica Technique.

PubMed

Segerström, Sofia; Wiking-Lima de Faria, Johanna; Braian, Michael; Ameri, Arman; Ahlgren, Camilla

2018-04-17

To validate the well-known and often-used impression replica technique for measuring fit between a preparation and a crown in vitro. The validation consisted of three steps. First, a measuring instrument was validated to elucidate its accuracy. Second, a specimen consisting of male and female counterparts was created and validated by the measuring instrument. Calculations were made for the exact values of three gaps between the male and female. Finally, impression replicas were produced of the specimen gaps and sectioned into four pieces. The replicas were then measured with the use of a light microscope. The values received from measuring the specimen were then compared with the values received from the impression replicas, and the technique was thereby validated. The impression replica technique overvalued all measured gaps. Depending on location of the three measuring sites, the difference between the specimen and the impression replicas varied from 47 to 130 μm. The impression replica technique overestimates gaps within the range of 2% to 11%. The validation of the replica technique enables the method to be used as a reference when testing other methods for evaluating fit in dentistry. © 2018 by the American College of Prosthodontists.

Fabrication of the replica templated from butterfly wing scales with complex light trapping structures

NASA Astrophysics Data System (ADS)

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

2015-11-01

The polydimethylsiloxane (PDMS) positive replica templated twice from the excellent light trapping surface of butterfly Trogonoptera brookiana wing scales was fabricated by a simple and promising route. The exact SiO2 negative replica was fabricated by using a synthesis method combining a sol-gel process and subsequent selective etching. Afterwards, a vacuum-aided process was introduced to make PDMS gel fill into the SiO2 negative replica, and the PDMS gel was solidified in an oven. Then, the SiO2 negative replica was used as secondary template and the structures in its surface was transcribed onto the surface of PDMS. At last, the PDMS positive replica was obtained. After comparing the PDMS positive replica and the original bio-template in terms of morphology, dimensions and reflectance spectra and so on, it is evident that the excellent light trapping structures of butterfly wing scales were inherited by the PDMS positive replica faithfully. This bio-inspired route could facilitate the preparation of complex light trapping nanostructure surfaces without any assistance from other power-wasting and expensive nanofabrication technologies.

Ground-based solar astrometric measurements during the PICARD mission

NASA Astrophysics Data System (ADS)

Irbah, A.; Meftah, M.; Corbard, T.; Ikhlef, R.; Morand, F.; Assus, P.; Fodil, M.; Lin, M.; Ducourt, E.; Lesueur, P.; Poiet, G.; Renaud, C.; Rouze, M.

2011-11-01

PICARD is a space mission developed mainly to study the geometry of the Sun. The satellite was launched in June 2010. The PICARD mission has a ground program which is based at the Calern Observatory (Observatoire de la C^ote d'Azur). It will allow recording simultaneous solar images from ground. Astrometric observations of the Sun using ground-based telescopes need however an accurate modelling of optical e®ects induced by atmospheric turbulence. Previous works have revealed a dependence of the Sun radius measurements with the observation conditions (Fried's parameter, atmospheric correlation time(s) ...). The ground instruments consist mainly in SODISM II, replica of the PICARD space instrument and MISOLFA, a generalized daytime seeing monitor. They are complemented by standard sun-photometers and a pyranometer for estimating a global sky quality index. MISOLFA is founded on the observation of Angle-of-Arrival (AA) °uctuations and allows us to analyze atmospheric turbulence optical e®ects on measurements performed by SODISM II. It gives estimations of the coherence parameters characterizing wave-fronts degraded by the atmospheric turbulence (Fried's parameter, size of the isoplanatic patch, the spatial coherence outer scale and atmospheric correlation times). This paper presents an overview of the ground based instruments of PICARD and some results obtained from observations performed at Calern observatory in 2011.

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.

Alternative Fuels Data Center: Semi Service Outfits Replica Batmobile to

Science.gov Websites

Run on Natural Gas Semi Service Outfits Replica Batmobile to Run on Natural Gas to someone by E -mail Share Alternative Fuels Data Center: Semi Service Outfits Replica Batmobile to Run on Natural Gas on Natural Gas on Twitter Bookmark Alternative Fuels Data Center: Semi Service Outfits Replica

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

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

Development of replicated optics for AXAF-1 XDA testing

NASA Technical Reports Server (NTRS)

Engelhaupt, Darell; Wilson, Michele; Martin, Greg

1995-01-01

Advanced optical systems for applications such as grazing incidence Wolter I x-ray mirror assemblies require extraordinary mirror surfaces in terms of fine finish and surface figure. The impeccable mirror surface is on the inside of the rotational mirror form. One practical method of producing devices with these requirements is to first fabricate an exterior surface for the optical device then replicate that surface to have the inverse component with lightweight characteristics. The replicated optic is not better than the master or mandrel from which it is made. This task identifies methods and materials for forming these extremely low roughness optical components. The objectives of this contract were to (1) prepare replication samples of electroless nickel coated aluminum, and determine process requirements for plating XDA test optic; (2) prepare and assemble plating equipment required to process a demonstration optic; (3) characterize mandrels, replicas and test samples for residual stress, surface contamination and surface roughness and figure using equipment at MSFC and; (4) provide technical expertise in establishing the processes, procedures, supplies and equipment needed to process the XDA test optics.

Characterization of Ultrafast Laser Pulses using a Low-dispersion Frequency Resolved Optical Grating Spectrometer

NASA Astrophysics Data System (ADS)

Whitelock, Hope; Bishop, Michael; Khosravi, Soroush; Obaid, Razib; Berrah, Nora

2016-05-01

A low dispersion frequency-resolved optical gating (FROG) spectrometer was designed to characterize ultrashort (<50 femtosecond) laser pulses from a commercial regenerative amplifier, optical parametric amplifier, and a home-built non-colinear optical parametric amplifier. This instrument splits a laser pulse into two replicas with a 90:10 intensity ratio using a thin pellicle beam-splitter and then recombines the pulses in a birefringent medium. The instrument detects a wavelength-sensitive change in polarization of the weak probe pulse in the presence of the stronger pump pulse inside the birefringent medium. Scanning the time delay between the two pulses and acquiring spectra allows for characterization of the frequency and time content of ultrafast laser pulses, that is needed for interpretation of experimental results obtained from these ultrafast laser systems. Funded by the DoE-BES, Grant No. DE-SC0012376.

High efficiency replicated x-ray optics and fabrication method

DOEpatents

Barbee, Jr., Troy W.; Lane, Stephen M.; Hoffman, Donald E.

2001-01-01

Replicated x-ray optics are fabricated by sputter deposition of reflecting layers on a super-polished reusable mandrel. The reflecting layers are strengthened by a supporting multilayer that results in stronger stress-relieved reflecting surfaces that do not deform during separation from the mandrel. The supporting multilayer enhances the ability to part the replica from the mandrel without degradation in surface roughness. The reflecting surfaces are comparable in smoothness to the mandrel surface. An outer layer is electrodeposited on the supporting multilayer. A parting layer may be deposited directly on the mandrel before the reflecting surface to facilitate removal of the layered, tubular optic device from the mandrel without deformation. The inner reflecting surface of the shell can be a single layer grazing reflection mirror or a resonant multilayer mirror. The resulting optics can be used in a wide variety of applications, including lithography, microscopy, radiography, tomography, and crystallography.

10 CFR 1.53 - Use of NRC seal or replicas.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Use of NRC seal or replicas. 1.53 Section 1.53 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION NRC Seal and Flag § 1.53 Use of NRC seal or replicas. (a) The use of the seal or replicas is restricted to the following: (1...

10 CFR 1.53 - Use of NRC seal or replicas.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Use of NRC seal or replicas. 1.53 Section 1.53 Energy NUCLEAR REGULATORY COMMISSION STATEMENT OF ORGANIZATION AND GENERAL INFORMATION NRC Seal and Flag § 1.53 Use of NRC seal or replicas. (a) The use of the seal or replicas is restricted to the following: (1...

Finite Size Corrections to the Parisi Overlap Function in the GREM

NASA Astrophysics Data System (ADS)

Derrida, Bernard; Mottishaw, Peter

2018-01-01

We investigate the effects of finite size corrections on the overlap probabilities in the Generalized Random Energy Model in two situations where replica symmetry is broken in the thermodynamic limit. Our calculations do not use replicas, but shed some light on what the replica method should give for finite size corrections. In the gradual freezing situation, which is known to exhibit full replica symmetry breaking, we show that the finite size corrections lead to a modification of the simple relations between the sample averages of the overlaps Y_k between k configurations predicted by replica theory. This can be interpreted as fluctuations in the replica block size with a negative variance. The mechanism is similar to the one we found recently in the random energy model in Derrida and Mottishaw (J Stat Mech 2015(1): P01021, 2015). We also consider a simultaneous freezing situation, which is known to exhibit one step replica symmetry breaking. We show that finite size corrections lead to full replica symmetry breaking and give a more complete derivation of the results presented in Derrida and Mottishaw (Europhys Lett 115(4): 40005, 2016) for the directed polymer on a tree.

Simulation studies of the fidelity of biomolecular structure ensemble recreation

NASA Astrophysics Data System (ADS)

Lätzer, Joachim; Eastwood, Michael P.; Wolynes, Peter G.

2006-12-01

We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm using input from "gold standard" reference ensembles that were first generated with a Gō-like Hamiltonian having nonpairwise additive terms. A set of low resolution data, which function as the "experimental" ϕ values, were first constructed from this reference ensemble. The resulting ϕ values were then treated as one would treat laboratory experimental data and were used as input in the replica reconstruction algorithm. The resulting ensembles of structures obtained by the replica algorithm were compared to the gold standard reference ensemble, from which those "data" were, in fact, obtained. It is found that for a unimodal transition state ensemble with a low barrier, the multiple replica algorithm does recreate the reference ensemble fairly successfully when no experimental error is assumed. The Kolmogorov-Smirnov test as well as principal component analysis show that the overlap of the recovered and reference ensembles is significantly enhanced when multiple replicas are used. Reduction of the multiple replica ensembles by clustering successfully yields subensembles with close similarity to the reference ensembles. On the other hand, for a high barrier transition state with two distinct transition state ensembles, the single replica algorithm only samples a few structures of one of the reference ensemble basins. This is due to the fact that the ϕ values are intrinsically ensemble averaged quantities. The replica algorithm with multiple copies does sample both reference ensemble basins. In contrast to the single replica case, the multiple replicas are constrained to reproduce the average ϕ values, but allow fluctuations in ϕ for each individual copy. These fluctuations facilitate a more faithful sampling of the reference ensemble basins. Finally, we test how robustly the reconstruction algorithm can function by introducing errors in ϕ comparable in magnitude to those suggested by some authors. In this circumstance we observe that the chances of ensemble recovery with the replica algorithm are poor using a single replica, but are improved when multiple copies are used. A multimodal transition state ensemble, however, turns out to be more sensitive to large errors in ϕ (if appropriately gauged) and attempts at successful recreation of the reference ensemble with simple replica algorithms can fall short.

Guidance of dorsal root ganglion neurites and Schwann cells by isolated Schwann cell topography on poly(dimethyl siloxane) conduits and films

NASA Astrophysics Data System (ADS)

Richardson, J. A.; Rementer, C. W.; Bruder, Jan M.; Hoffman-Kim, D.

2011-08-01

Biomimetic replicas of cellular topography have been utilized to direct neurite outgrowth. Here, we cultured postnatal rat dorsal root ganglion (DRG) explants in the presence of Schwann cell (SC) topography to determine the influence of SC topography on neurite outgrowth. Four distinct poly(dimethyl siloxane) conduits were fabricated within which DRG explants were cultured. To determine the contribution of SC topographical features to neurite guidance, the extent of neurite outgrowth into unpatterned conduits, conduits with randomly oriented SC replicas, and conduits with SC replicas parallel or perpendicular to the conduit long axis was measured. Neurite directionality and outgrowth from DRG were also quantified on two-dimensional SC replicas with orientations corresponding to the four conduit conditions. Additionally, live SC migration and neurite extension from DRG on SC replicas were examined as a first step toward quantification of the interactions between live SC and navigating neurites on SC replicas. DRG neurite outgrowth and morphology within conduits and on two-dimensional SC replicas were directed by the underlying SC topographical features. Maximal neurite outgrowth and alignment to the underlying features were observed into parallel conduits and on parallel two-dimensional substrates, whereas the least extent of outgrowth was observed into perpendicular conduits and on perpendicular two-dimensional replica conditions. Additionally, neurites on perpendicular conditions turned to extend along the direction of underlying SC topography. Neurite outgrowth exceeded SC migration in the direction of the underlying anisotropic SC replica after two days in culture. This finding confirms the critical role that SC have in guiding neurite outgrowth and suggests that the mechanism of neurite alignment to SC replicas depends on direct contact with cellular topography. These results suggest that SC topographical replicas may be used to direct and optimize neurite alignment, and emphasize the importance of SC features in neurite guidance.

Polarized quantum dot emission in electrohydrodynamic jet printed photonic crystals

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

See, Gloria G.; Xu, Lu; Nuzzo, Ralph G.

2015-08-03

Tailored optical output, such as color purity and efficient optical intensity, are critical considerations for displays, particularly in mobile applications. To this end, we demonstrate a replica molded photonic crystal structure with embedded quantum dots. Electrohydrodynamic jet printing is used to control the position of the quantum dots within the device structure. This results in significantly less waste of the quantum dot material than application through drop-casting or spin coating. In addition, the targeted placement of the quantum dots minimizes any emission outside of the resonant enhancement field, which enables an 8× output enhancement and highly polarized emission from themore » photonic crystal structure.« less

Replication of self-centering optical fiber alignment structures using hot embossing

NASA Astrophysics Data System (ADS)

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

2016-04-01

With the demand for broadband connectivity on the rise due to various services like video-on-demand and cloud computing becoming more popular, the need for better connectivity infrastructure is high. The only future- proof option to supply this infrastructure is to deploy "fiber to the home" (FTTH) networks. One of the main difficulties with the deployment of FTTH is the vast amount of single-mode fiber (SMF) connections that need to be made. Hence there is a strong need for components which enable high performance, robust and easy-to- use SMF connectors. Since large-scale deployment is the goal, these components should be mass-producible at low cost. We discuss a rapid prototyping process on the basis of hot embossing replication of a self-centering alignment system (SCAS) based on three micro-springs, which can position a SMF independently of its diameter. This is beneficial since there is a fabrication tolerance of up to +/-1 μm on a standard G.652 SMF's diameter that can lead to losses if the outer diameter is used as a reference for alignment. The SCAS is first prototyped with deep proton writing (DPW) in polymethylmethacrylate (PMMA) after which it is glued to a copper substrate with an adhesive. Using an electroforming process, a nickel block is grown over the PMMA prototype followed by mechanical finishing to fabricate a structured nickel mould insert. Even though the mould insert shows non- ideal and rounded features it is used to create PMMA replicas of the SCAS by means of hot embossing. The SCAS possesses a central opening in which a bare SMF can be clamped, which is designed with a diameter of 121 μm. PMMA replicas are dimensionally characterized using a multisensor coordinate measurement machine and show a central opening diameter of 128.3 +/- 2.8 μm. This should be compared to the central opening diameter of the DPW prototype used for mould formation which was measured to be 120.5 μm. This shows that the electroforming and subsequent replication process is possible for complex micro-scale components and could be accurate after optimisation. We characterized the sidewall roughness of PMMA replicas using a non- contact optical profiler, resulting in a root-mean-square roughness of 48 nm over an area of 63.7 μm×47.8 μm. This low sidewall roughness is especially important in the replication of high aspect ratio structures to facilitate demoulding since the sidewalls cause the most friction with the mould insert.

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.

Population control of self-replicating systems

NASA Technical Reports Server (NTRS)

Mccord, R. L.

1982-01-01

The literature concerning fibonacci sequence and the mathematics of self replication are reviewed. One option allows each primary to generate n-replicas, one in each sequential time frame after its own generation with no restrictions on the number of ancestors per replica. The state vector of the replicas in an efficient manner is determined. Option-B has a fixed number of replicas per primary and no restrictions on the number of ancestors for a replica. Any element fij represents the number of elements of type-j in time frame k+1 generated from type-i in time frame k. Option-D is a diagonal matrix whose eigenvalues are precisely those of f.

(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

Mimicking the colourful wing scale structure of the Papilio blumei butterfly.

PubMed

Kolle, Mathias; Salgard-Cunha, Pedro M; Scherer, Maik R J; Huang, Fumin; Vukusic, Pete; Mahajan, Sumeet; Baumberg, Jeremy J; Steiner, Ullrich

2010-07-01

The brightest and most vivid colours in nature arise from the interaction of light with surfaces that exhibit periodic structure on the micro- and nanoscale. In the wings of butterflies, for example, a combination of multilayer interference, optical gratings, photonic crystals and other optical structures gives rise to complex colour mixing. Although the physics of structural colours is well understood, it remains a challenge to create artificial replicas of natural photonic structures. Here we use a combination of layer deposition techniques, including colloidal self-assembly, sputtering and atomic layer deposition, to fabricate photonic structures that mimic the colour mixing effect found on the wings of the Indonesian butterfly Papilio blumei. We also show that a conceptual variation to the natural structure leads to enhanced optical properties. Our approach offers improved efficiency, versatility and scalability compared with previous approaches.

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

Dong Yuli; Zou Xubo; Guo Guangcan

We investigate the economical Gaussian cloning of coherent states with the known phase, which produces M copies from N input replica and can be implemented with degenerate parametric amplifiers and beam splitters.The achievable fidelity of single copy is given by 2M{radical}(N)/[{radical}(N)(M-1)+{radical}((1+N)(M{sup 2}+N))], which is bigger than the optimal fidelity of the universal Gaussian cloning. The cloning machine presented here works without ancillary optical modes and can be regarded as the continuous variable generalization of the economical cloning machine for qudits.

Application Of Holographic Interferometry For Investigation Of Microroughness Of Engineering Surfaces

NASA Astrophysics Data System (ADS)

Lech, Marek; Mruk, Irena; Stupnicki, Jacek

1985-01-01

The paper describes an improved immersion method of holographic interferometry /IMHI/ adjusted for studies of roughness of engineering surfaces. Special optical arrangement, with two types of immersion cells and adequate technique of preparing transparent replicas reproducting with high fidelity details of differently machined surfaces was elaborated. It permits to obtain the contour maps of the surface asperities with intervals between the planes of succesive contour lines within a range of 1 μm. The results obtained for some engineering surfaces are given.

Holmium:YAG thermokeratoplasty: treatment parameters for the correction of astigmatism based upon enucleated human eyes using an application mask

NASA Astrophysics Data System (ADS)

Kriegerowski, Martin; Rassmann, Katja; Oltrup, Theo; Bende, Thomas; Jean, Benedikt J.

1995-05-01

The refractive outcome of thermokeratoplasty depends upon the location and angle of the coagulation spots, applied with a focusing handpiece onto the corneal surface. Accuracy can be enhanced using a specially designed application mask. An astigmatism correction was performed on 10 human donor eyes (Holmium 25, Technomed, FRG, 15 Hz, 20 mJ/pulse, 25 pulses) with an optical zone of 8.1 mm, 5 eyes received a free hand laser application (marked positions) and the other 5 eyes were treated using a suctioned metal mask with drills for the handpiece (optical zone 8.1 mm). To compare the results a silicone replica was taken and analyzed by a confocal laser microtopometer. The refractive change for the steepest meridian was 10 D with a standard deviation of +/- 3.7 D for the free hand application. Using the application mask the refractive outcome was 9.8 D with a standard deviation of only 0.8 D. Using the application mask the standard deviation for the induced refractive change decreases by a factor of five.

Overview of diffraction gratings technologies for space-flight satellites and astronomy

NASA Astrophysics Data System (ADS)

Cotel, Arnaud; Liard, Audrey; Desserouer, Frédéric; Bonnemason, Francis; Pichon, Pierre

2014-09-01

The diffraction gratings are widely used in Space-flight satellites for spectrograph instruments or in ground-based telescopes in astronomy. The diffraction gratings are one of the key optical components of such systems and have to exhibit very high optical performances. HORIBA Jobin Yvon S.A.S. (part of HORIBA Group) is in the forefront of such gratings development for more than 40 years. During the past decades, HORIBA Jobin Yvon (HJY) has developed a unique expertise in diffraction grating design and manufacturing processes for holographic, ruled or etched gratings. We will present in this paper an overview of diffraction grating technologies especially designed for space and astronomy applications. We will firstly review the heritage of the company in this field with the space qualification of different grating types. Then, we will describe several key grating technologies developed for specific space or astronomy projects: ruled blazed low groove density plane reflection grating, holographic blazed replica plane grating, high-groove density holographic toroidal and spherical grating and transmission Fused Silica Etched (FSE) grismassembled grating.

The flower of Hibiscus trionum is both visibly and measurably iridescent.

PubMed

Vignolini, Silvia; Moyroud, Edwige; Hingant, Thomas; Banks, Hannah; Rudall, Paula J; Steiner, Ullrich; Glover, Beverley J

2015-01-01

Living organisms can use minute structures to manipulate the reflection of light and display colours based on interference. There has been debate in recent literature over whether the diffractive optical effects produced by epoxy replicas of petals with folded cuticles persist and induce iridescence in the original flowers when the effects of petal pigment and illumination are taken into account. We explored the optical properties of the petal of Hibiscus trionum by macro-imaging, scanning and transmission electron microscopy, and visible and ultraviolet (UV) angle-resolved spectroscopy of the petal. The flower of Hibiscus trionum is visibly iridescent, and the iridescence can be captured photographically. The iridescence derives from a diffraction grating generated by folds of the cuticle. The iridescence of the petal can be quantitatively characterized by spectrometric measurements with several square-millimetres of sample area illuminated. The flower of Hibiscus trionum has the potential to interact with its pollinators (honeybees, other bees, butterflies and flies) through iridescent signals produced by its cuticular diffraction grating. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

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.

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.

Internal structure analysis of particle-double network gels used in a gel organ replica

NASA Astrophysics Data System (ADS)

Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

2016-04-01

In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

Optical properties of ZnO powder prepared by using a proteic sol-gel process

NASA Astrophysics Data System (ADS)

Kwon, Bong-Joon; Woo, Hyun-Joo; Park, Ji-Yeon; Jang, Kiwan; Lim, Seung-Hyuk; Cho, Yong-Hoon

2013-03-01

We have studied the optical properties of ZnO powder synthesized by using a proteic sol-gel process with coconut water as the precursor. The energy dispersive X-ray spectrometer and X-ray diffraction results show high purity of the synthesized ZnO powder. From the low-temperature (12 K) and power-dependent PL spectra, the donor-bound exciton, the acceptor-bound exciton, the donor-to-acceptor pair (DAP), and the phonon-replica of the DAP transition have been observed at 3.38, 3.34, 3.26, and 3.19 eV, respectively. The free exciton emission (˜3.3 eV) is also observed at 300 K in the temperature-dependent PL spectra.

Embedding objects during 3D printing to add new functionalities.

PubMed

Yuen, Po Ki

2016-07-01

A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning(®) Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication. These 3D printed glass bottom casting molds would result in PDMS replicas with a flat smooth bottom surface for better bonding and adhesion.

Angle-selective optical filter for highly sensitive reflection photoplethysmogram

PubMed Central

Hwang, Chan-Sol; Yang, Sung-Pyo; Jang, Kyung-Won; Park, Jung-Woo; Jeong, Ki-Hun

2017-01-01

We report an angle-selective optical filter (ASOF) for highly sensitive reflection photoplethysmography (PPG) sensors. The ASOF features slanted aluminum (Al) micromirror arrays embedded in transparent polymer resin, which effectively block scattered light under human tissue. The device microfabrication was done by using geometry-guided resist reflow of polymer micropatterns, polydimethylsiloxane replica molding, and oblique angle deposition of thin Al film. The angular transmittance through the ASOF is precisely controlled by the angle of micromirrors. For the mirror angle of 30 degrees, the ASOF accepts an incident light between - 90 to + 50 degrees and the maximum transmittance at - 55 degrees. The ASOF exhibits the substantial reduction of both the in-band noise of PPG signals over a factor of two and the low-frequency noise by three times. Consequently, this filter allows distinguishing the diastolic peak that allows miscellaneous parameters with diverse vascular information. This optical filter provides a new opportunity for highly sensitive PPG monitoring or miscellaneous optical tomography. PMID:29082070

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

Replica amplification of nucleic acid arrays

DOEpatents

Church, George M.; Mitra, Robi D.

2010-08-31

Disclosed are improved methods of making and using immobilized arrays of nucleic acids, particularly methods for producing replicas of such arrays. Included are methods for producing high density arrays of nucleic acids and replicas of such arrays, as well as methods for preserving the resolution of arrays through rounds of replication. Also included are methods which take advantage of the availability of replicas of arrays for increased sensitivity in detection of sequences on arrays. Improved methods of sequencing nucleic acids immobilized on arrays utilizing single copies of arrays and methods taking further advantage of the availability of replicas of arrays are disclosed. The improvements lead to higher fidelity and longer read lengths of sequences immobilized on arrays. Methods are also disclosed which improve the efficiency of multiplex PCR using arrays of immobilized nucleic acids.

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.

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.

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

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.

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.

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.

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).

Cheap and fast measuring roughness on big surfaces with an imprint method

NASA Astrophysics Data System (ADS)

Schopf, C.; Liebl, J.; Rascher, R.

2017-10-01

Roughness, shape and structure of a surface offer information on the state, shape and surface characteristics of a component. Particularly the roughness of the surface dictates the subsequent polishing of the optical surface. The roughness is usually measured by a white light interferometer, which is limited by the size of the components. Using a moulding method of surfaces that are difficult to reach, an imprint is taken and analysed regarding to roughness and structure. This moulding compound method is successfully used in dental technology. In optical production, the moulding compound method is advantageous in roughness determination in inaccessible spots or on large components (astrological optics). The "replica method" has been around in metal analysis and processing. Film is used in order to take an impression of a surface. Then, it is analysed for structures. In optical production, compound moulding seems advantageous in roughness determination in inaccessible spots or on large components (astrological optics). In preliminary trials, different glass samples with different roughness levels were manufactured. Imprints were taken from these samples (based on DIN 54150 "Abdruckverfahren für die Oberflächenprüfung"). The objective of these feasibility tests was to determine the limits of this method (smallest roughness determinable / highest roughness). The roughness of the imprint was compared with the roughness of the glass samples. By comparing the results, the uncertainty of the measuring method was determined. The spectrum for the trials ranged from rough grind (0.8 μm rms), over finishing grind (0.6 μm rms) to polishing (0.1 μm rms).

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.

Physical and Optical/Radiative Characteristics of Aerosol and Cloud Particles in Tropical Cirrus: Importance in Radiation Balance

NASA Technical Reports Server (NTRS)

Pueschel, R. F.; Howard, S. D.; Foster, T. C.; Hallett, J.; Arnott, W. P.; Condon, Estelle P. (Technical Monitor)

1996-01-01

Whether cirrus clouds heat or cool the Earth-atmosphere system depends on the relative importance of the cloud shortwave albedo effect and the cloud thermal greenhouse effect. Both are determined by the distribution of ice condensate with cloud particle size. The microphysics instrument package flown aboard the NASA DC-8 in TOGA/COARE included an ice crystal replicator, a 2D Greyscale Cloud Particle Probe and a Forward Scattering Spectrometer Aerosol Probe. In combination, the electro-optical instruments permitted particle size measurements between 0.5 micrometer and 2.6 millimeter diameter. Ice crystal replicas were used to validate signals from the electrooptical instruments. Both optical and scanning electron microscopy were utilized to analyze aerosol and ice particle replicas between 0.1 micrometer and several 100 micrometer diameter. In first approximation, the combined aerosol-cloud particle spectrum in several clouds followed a power law N alpha D(sup -2.5). Thus, large cloud particles carried most of the condensate mass, while small cloud and aerosol particles determined the surface area. The mechanism of formation of small particles is growth of (hygroscopic, possibly ocean-derived) aerosol particles along the Kohler curves. The concentration of small particles is higher and less variable in space and time, and their tropospheric residence time is longer, than those of large cloud particles because of lower sedimentation velocities. Small particles shift effective cloud particle radii to sizes much smaller than the mean diameter of the cloud particles. This causes an increase in shortwave reflectivity and IR emissivity, and a decrease in transmissivity. Occasionally, the cloud reflectivity increased with altitude (decreasing temperature) stronger than did cloud emissivity, yielding enhanced radiative cooling at higher altitudes. Thus, cirrus produced by deep convection in the tropics may be critical in controlling processes whereby energy from warm tropical oceans is injected to different levels in the atmosphere to subsequently influence not only tropical but mid-latitude climate.

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.

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 \

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.

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

Emission spectra of a laser based on an In(Ga)As/GaAs quantum-dot superlattice

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

Sobolev, M. M., E-mail: m.sobolev@mail.ioffe.ru; Buyalo, M. S.; Nevedomskiy, V. N.

2015-10-15

The spectral characteristics of a laser with an active region based on a ten-layer system of In(Ga)As/GaAs vertically correlated quantum dots with 4.5-nm GaAs spacer layers between InAs quantum dots are studied under the conditions of spontaneous and stimulated emission, depending on the current and the duration of pump pulses. Data obtained by transmission electron microscopy and electroluminescence and absorption polarization anisotropy measurements make it possible to demonstrate that the investigated system of tunnel-coupled InAs quantum dots separated by thin GaAs barriers represents a quantum-dot superlattice. With an increase in the laser pump current, the electroluminescence intensity increases linearly andmore » the spectral position of the electroluminescence maximum shifts to higher energies, which is caused by the dependence of the miniband density-of-states distribution on the pump current. Upon exceeding the threshold current, multimode lasing via the miniband ground state is observed. One of the lasing modes can be attributed to the zero-phonon line, and the other is determined by the longitudinal-optical phonon replica of quantum-dot emission. The results obtained give evidence that, under conditions of the laser pumping of an In(Ga)As/GaAs quantum-dot superlattice, strong coupling between the discrete electron states in the miniband and optical phonons takes place. This leads to the formation of quantum-dot polarons, resulting from the resonant mixing of electronic states whose energy separation is comparable to the optical-phonon energy.« less

Two-step phase-shifting SPIDER

NASA Astrophysics Data System (ADS)

Zheng, Shuiqin; Cai, Yi; Pan, Xinjian; Zeng, Xuanke; Li, Jingzhen; Li, Ying; Zhu, Tianlong; Lin, Qinggang; Xu, Shixiang

2016-09-01

Comprehensive characterization of ultrafast optical field is critical for ultrashort pulse generation and its application. This paper combines two-step phase-shifting (TSPS) into the spectral phase interferometry for direct electric-field reconstruction (SPIDER) to improve the reconstruction of ultrafast optical-fields. This novel SPIDER can remove experimentally the dc portion occurring in traditional SPIDER method by recording two spectral interferograms with π phase-shifting. As a result, the reconstructed results are much less disturbed by the time delay between the test pulse replicas and the temporal widths of the filter window, thus more reliable. What is more, this SPIDER can work efficiently even the time delay is so small or the measured bandwidth is so narrow that strong overlap happens between the dc and ac portions, which allows it to be able to characterize the test pulses with complicated temporal/spectral structures or narrow bandwidths.

Grisms Developed for FOCAS

NASA Astrophysics Data System (ADS)

Ebizuka, Noboru; Kawabata, Koji S.; Oka, Keiko; Yamada, Akiko; Kashiwagi, Masako; Kodate, Kashiko; Hattori, Takashi; Kashikawa, Nobunari; Iye, Masanori

2011-03-01

Faint Object Camera and Spectrograph (FOCAS) is a versatile common-use optical instrument for the 8.2 m Subaru Telescope, offering imaging and spectroscopic observations. FOCAS employs grisms with resolving powers ranging from 280 to 8200 as dispersive optical elements. A grism is a direct-vision grating composed of a transmission grating and prism(s). FOCAS has five grisms with replica surface-relief gratings including an echelle-type grism, and eight grisms with volume-phase holographic (VPH) gratings. The size of these grisms is 110 mm × 106 mm in aperture with a maximum thickness of 110 mm. We employ not only the dichromated gelatin, but also the hologram resin as a recording material for VPH gratings. We discuss the performance of these FOCAS grisms measured in the laboratory, and verify it by test observations, and show examples of astronomical spectroscopic observations.

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

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

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.

An assessment of multimodal imaging of subsurface text in mummy cartonnage using surrogate papyrus phantoms

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

Gibson, Adam; Piquette, Kathryn E.; Bergmann, Uwe

Ancient Egyptian mummies were often covered with an outer casing, panels and masks made from cartonnage: a lightweight material made from linen, plaster, and recycled papyrus held together with adhesive. Egyptologists, papyrologists, and historians aim to recover and read extant text on the papyrus contained within cartonnage layers, but some methods, such as dissolving mummy casings, are destructive. The use of an advanced range of different imaging modalities was investigated to test the feasibility of non-destructive approaches applied to multi-layered papyrus found in ancient Egyptian mummy cartonnage. Eight different techniques were compared by imaging four synthetic phantoms designed to providemore » robust, well-understood, yet relevant sample standards using modern papyrus and replica inks. The techniques include optical (multispectral imaging with reflection and transillumination, and optical coherence tomography), X-ray (X-ray fluorescence imaging, X-ray fluorescence spectroscopy, X-ray micro computed tomography and phase contrast X-ray) and terahertz-based approaches. Optical imaging techniques were able to detect inks on all four phantoms, but were unable to significantly penetrate papyrus. X-ray-based techniques were sensitive to iron-based inks with excellent penetration but were not able to detect carbon-based inks. However, using terahertz imaging, it was possible to detect carbon-based inks with good penetration but with less sensitivity to iron-based inks. The phantoms allowed reliable and repeatable tests to be made at multiple sites on three continents. Finally, the tests demonstrated that each imaging modality needs to be optimised for this particular application: it is, in general, not sufficient to repurpose an existing device without modification. Furthermore, it is likely that no single imaging technique will to be able to robustly detect and enable the reading of text within ancient Egyptian mummy cartonnage. However, by carefully selecting, optimising and combining techniques, text contained within these fragile and rare artefacts may eventually be open to non-destructive imaging, identification, and interpretation.« less

An assessment of multimodal imaging of subsurface text in mummy cartonnage using surrogate papyrus phantoms

DOE PAGES

Gibson, Adam; Piquette, Kathryn E.; Bergmann, Uwe; ...

2018-02-26

Ancient Egyptian mummies were often covered with an outer casing, panels and masks made from cartonnage: a lightweight material made from linen, plaster, and recycled papyrus held together with adhesive. Egyptologists, papyrologists, and historians aim to recover and read extant text on the papyrus contained within cartonnage layers, but some methods, such as dissolving mummy casings, are destructive. The use of an advanced range of different imaging modalities was investigated to test the feasibility of non-destructive approaches applied to multi-layered papyrus found in ancient Egyptian mummy cartonnage. Eight different techniques were compared by imaging four synthetic phantoms designed to providemore » robust, well-understood, yet relevant sample standards using modern papyrus and replica inks. The techniques include optical (multispectral imaging with reflection and transillumination, and optical coherence tomography), X-ray (X-ray fluorescence imaging, X-ray fluorescence spectroscopy, X-ray micro computed tomography and phase contrast X-ray) and terahertz-based approaches. Optical imaging techniques were able to detect inks on all four phantoms, but were unable to significantly penetrate papyrus. X-ray-based techniques were sensitive to iron-based inks with excellent penetration but were not able to detect carbon-based inks. However, using terahertz imaging, it was possible to detect carbon-based inks with good penetration but with less sensitivity to iron-based inks. The phantoms allowed reliable and repeatable tests to be made at multiple sites on three continents. Finally, the tests demonstrated that each imaging modality needs to be optimised for this particular application: it is, in general, not sufficient to repurpose an existing device without modification. Furthermore, it is likely that no single imaging technique will to be able to robustly detect and enable the reading of text within ancient Egyptian mummy cartonnage. However, by carefully selecting, optimising and combining techniques, text contained within these fragile and rare artefacts may eventually be open to non-destructive imaging, identification, and interpretation.« less

Embedding objects during 3D printing to add new functionalities

PubMed Central

2016-01-01

A novel method for integrating and embedding objects to add new functionalities during 3D printing based on fused deposition modeling (FDM) (also known as fused filament fabrication or molten polymer deposition) is presented. Unlike typical 3D printing, FDM-based 3D printing could allow objects to be integrated and embedded during 3D printing and the FDM-based 3D printed devices do not typically require any post-processing and finishing. Thus, various fluidic devices with integrated glass cover slips or polystyrene films with and without an embedded porous membrane, and optical devices with embedded Corning® Fibrance™ Light-Diffusing Fiber were 3D printed to demonstrate the versatility of the FDM-based 3D printing and embedding method. Fluid perfusion flow experiments with a blue colored food dye solution were used to visually confirm fluid flow and/or fluid perfusion through the embedded porous membrane in the 3D printed fluidic devices. Similar to typical 3D printed devices, FDM-based 3D printed devices are translucent at best unless post-polishing is performed and optical transparency is highly desirable in any fluidic devices; integrated glass cover slips or polystyrene films would provide a perfect optical transparent window for observation and visualization. In addition, they also provide a compatible flat smooth surface for biological or biomolecular applications. The 3D printed fluidic devices with an embedded porous membrane are applicable to biological or chemical applications such as continuous perfusion cell culture or biocatalytic synthesis but without the need for any post-device assembly and finishing. The 3D printed devices with embedded Corning® Fibrance™ Light-Diffusing Fiber would have applications in display, illumination, or optical applications. Furthermore, the FDM-based 3D printing and embedding method could also be utilized to print casting molds with an integrated glass bottom for polydimethylsiloxane (PDMS) device replication. These 3D printed glass bottom casting molds would result in PDMS replicas with a flat smooth bottom surface for better bonding and adhesion. PMID:27478528

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.

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.

A fractographic study of clinically retrieved zirconia-ceramic and metal-ceramic fixed dental prostheses.

PubMed

Pang, Zhen; Chughtai, Asima; Sailer, Irena; Zhang, Yu

2015-10-01

A recent 3-year randomized controlled trial (RCT) of tooth supported three- to five-unit zirconia-ceramic and metal-ceramic posterior fixed dental prostheses (FDPs) revealed that veneer chipping and fracture in zirconia-ceramic systems occurred more frequently than those in metal-ceramic systems [1]. This study seeks to elucidate the underlying mechanisms responsible for the fracture phenomena observed in this RCT using a descriptive fractographic analysis. Vinyl-polysiloxane impressions of 12 zirconia-ceramic and 6 metal-ceramic FDPs with veneer fractures were taken from the patients at the end of a mean observation of 40.3±2.8 months. Epoxy replicas were produced from these impressions [1]. All replicas were gold coated, and inspected under the optical microscope and scanning electron microscope (SEM) for descriptive fractography. Among the 12 zirconia-ceramic FDPs, 2 had small chippings, 9 had large chippings, and 1 exhibited delamination. Out of 6 metal-ceramic FDPs, 5 had small chippings and 1 had large chipping. Descriptive fractographic analysis based on SEM observations revealed that fracture initiated from the wear facet at the occlusal surface in all cases, irrespective of the type of restoration. Zirconia-ceramic and metal-ceramic FDPs all fractured from microcracks that emanated from occlusal wear facets. The relatively low fracture toughness and high residual tensile stress in porcelain veneer of zirconia restorations may contribute to the higher chipping rate and larger chip size in zirconia-ceramic FDPs relative to their metal-ceramic counterparts. The low veneer/core interfacial fracture energy of porcelain-veneered zirconia may result in the occurrence of delamination in zirconia-ceramic FDPs. Copyright © 2015 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

A fractographic study of clinically retrieved zirconia–ceramic and metal–ceramic fixed dental prostheses

PubMed Central

Pang, Zhen; Chughtai, Asima; Sailer, Irena; Zhang, Yu

2015-01-01

Objectives A recent 3-year randomized controlled trial (RCT) of tooth supported three- to five-unit zirconia–ceramic and metal–ceramic posterior fixed dental prostheses (FDPs) revealed that veneer chipping and fracture in zirconia–ceramic systems occurred more frequently than those in metal–ceramic systems [1]. This study seeks to elucidate the underlying mechanisms responsible for the fracture phenomena observed in this RCT using a descriptive fractographic analysis. Methods Vinyl-polysiloxane impressions of 12 zirconia–ceramic and 6 metal–ceramic FDPs with veneer fractures were taken from the patients at the end of a mean observation of 40.3 ± 2.8 months. Epoxy replicas were produced from these impressions [1]. All replicas were gold coated, and inspected under the optical microscope and scanning electron microscope (SEM) for descriptive fractography. Results Among the 12 zirconia–ceramic FDPs, 2 had small chippings, 9 had large chippings, and 1 exhibited delamination. Out of 6 metal–ceramic FDPs, 5 had small chippings and 1 had large chipping. Descriptive fractographic analysis based on SEM observations revealed that fracture initiated from the wear facet at the occlusal surface in all cases, irrespective of the type of restoration. Significance Zirconia–ceramic and metal–ceramic FDPs all fractured from microcracks that emanated from occlusal wear facets. The relatively low fracture toughness and high residual tensile stress in porcelain veneer of zirconia restorations may contribute to the higher chipping rate and larger chip size in zirconia–ceramic FDPs relative to their metal–ceramic counterparts. The low veneer/core interfacial fracture energy of porcelain-veneered zirconia may result in the occurrence of delamination in zirconia–ceramic FDPs. PMID:26233469

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

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.

Antagonist wear of monolithic zirconia crowns after 2 years.

PubMed

Lohbauer, Ulrich; Reich, Sven

2017-05-01

The aim of this study was to evaluate the amount of wear on the antagonist occlusal surfaces of clinically placed monolithic zirconia premolar and molar crowns (LAVA Plus, 3M ESPE). Fourteen in situ monolithic zirconia crowns and their opposing antagonists (n = 26) are the subject of an ongoing clinical trial and have been clinically examined at baseline and after 24 months. Silicone impressions were taken and epoxy replicas produced for qualitative SEM analysis and quantitative analysis using optical profilometry. Based on the baseline replicas, the follow-up situation has been scanned and digitally matched with the initial topography in order to calculate the mean volume loss (in mm 3 ) as well as the mean maximum vertical loss (in mm) after 2 years in service. The mean volume loss for enamel antagonist contacts (n = 7) was measured to 0.361 mm 3 and the mean of the maximum vertical loss to 0.204 mm. The mean volume loss for pure ceramic contacts (n = 10) was measured to 0.333 mm 3 and the mean of the maximum vertical loss to 0.145 mm. The wear rates on enamel contacts were not significantly different from those measured on ceramic antagonists. Based on the limitations of this study, it can be concluded for the monolithic zirconia material LAVA Plus that the measured wear rates are in consensus with other in vivo studies on ceramic restorations. Further, that no significant difference was found between natural enamel antagonists and ceramic restorations as antagonists. The monolithic zirconia restorations do not seem to be affected by wear within the first 2 years. The monolithic zirconia crowns (LAVA Plus) show acceptable antagonist wear rates after 2 years in situ, regardless of natural enamel or ceramics as antagonist materials.

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.

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)

Nanostructured Diamond Device for Biomedical Applications.

PubMed

Fijalkowski, M; Karczemska, A; Lysko, J M; Zybala, R; KozaneckI, M; Filipczak, P; Ralchenko, V; Walock, M; Stanishevsky, A; Mitura, S

2015-02-01

Diamond is increasingly used in biomedical applications because of its unique properties such as the highest thermal conductivity, good optical properties, high electrical breakdown voltage as well as excellent biocompatibility and chemical resistance. Diamond has also been introduced as an excellent substrate to make the functional microchip structures for electrophoresis, which is the most popular separation technique for the determination of analytes. In this investigation, a diamond electrophoretic chip was manufactured by a replica method using a silicon mold. A polycrystalline 300 micron-thick diamond layer was grown by the microwave plasma-assisted CVD (MPCVD) technique onto a patterned silicon substrate followed by the removal of the substrate. The geometry of microstructure, chemical composition, thermal and optical properties of the resulting free-standing diamond electrophoretic microchip structure were examined by CLSM, SFE, UV-Vis, Raman, XRD and X-ray Photoelectron Spectroscopy, and by a modified laser flash method for thermal property measurements.

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.

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.

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.

An efficient way of high-contrast, quasi-3D cellular imaging: off-axis illumination.

PubMed

Hostounský, Zdenĕk; Pelc, Radek

2006-07-31

An imaging system enabling a convenient visualisation of cells and other small objects is presented. It represents an adaptation of the optical microscope condenser, accommodating a built-in edge (relief) diaphragm brought close to the condenser iris diaphragm and enabling high-contrast pseudo-relief (quasi-3D) imaging. The device broadens the family of available apparatus based on the off-axis (or anaxial, asymmetric, inclined, oblique, schlieren-type, sideband) illumination. The simplicity of the design makes the condenser a user-friendly, dedicated device delivering high-contrast quasi-3D images of phase objects. Those are nearly invisible under the ordinary (axial) illumination. The phase contrast microscopy commonly used in visualisation of phase objects does not deliver the quasi-3D effect and introduces a disturbing 'halo' effect around the edges. The performance of the device presented here is demonstrated on living cells and tissue replicas. High-contrast quasi-3D images of cell-free preparations of biological origin (paper fibres and microcrystals) are shown as well.

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.

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

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/).

Development of an automated data acquisition and processing pipeline using multiple telescopes for observing transient phenomena

NASA Astrophysics Data System (ADS)

Savant, Vaibhav; Smith, Niall

2016-07-01

We report on the current status in the development of a pilot automated data acquisition and reduction pipeline based around the operation of two nodes of remotely operated robotic telescopes based in California, USA and Cork, Ireland. The observatories are primarily used as a testbed for automation and instrumentation and as a tool to facilitate STEM (Science Technology Engineering Mathematics) promotion. The Ireland node is situated at Blackrock Castle Observatory (operated by Cork Institute of Technology) and consists of two optical telescopes - 6" and 16" OTAs housed in two separate domes while the node in California is its 6" replica. Together they form a pilot Telescope ARrAy known as TARA. QuickPhot is an automated data reduction pipeline designed primarily to throw more light on the microvariability of blazars employing precision optical photometry and using data from the TARA telescopes as they constantly monitor predefined targets whenever observing conditions are favourable. After carrying out aperture photometry, if any variability above a given threshold is observed, the reporting telescope will communicate the source concerned and the other nodes will follow up with multi-band observations, taking advantage that they are located in strategically separated time-zones. Ultimately we wish to investigate the applicability of Shock-in-Jet and Geometric models. These try to explain the processes at work in AGNs which result in the formation of jets, by looking for temporal and spectral variability in TARA multi-band observations. We are also experimenting with using a Twochannel Optical PHotometric Imaging CAMera (TOΦCAM) that we have developed and which has been optimised for simultaneous two-band photometry on our 16" OTA.

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.

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.

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.

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

Aging and visual 3-D shape recognition from motion.

PubMed

Norman, J Farley; Adkins, Olivia C; Dowell, Catherine J; Hoyng, Stevie C; Shain, Lindsey M; Pedersen, Lauren E; Kinnard, Jonathan D; Higginbotham, Alexia J; Gilliam, Ashley N

2017-11-01

Two experiments were conducted to evaluate the ability of younger and older adults to recognize 3-D object shape from patterns of optical motion. In Experiment 1, participants were required to identify dotted surfaces that rotated in depth (i.e., surface structure portrayed using the kinetic depth effect). The task difficulty was manipulated by limiting the surface point lifetimes within the stimulus apparent motion sequences. In Experiment 2, the participants identified solid, naturally shaped objects (replicas of bell peppers, Capsicum annuum) that were defined by occlusion boundary contours, patterns of specular highlights, or combined optical patterns containing both boundary contours and specular highlights. Significant and adverse effects of increased age were found in both experiments. Despite the fact that previous research has found that increases in age do not reduce solid shape discrimination, our current results indicated that the same conclusion does not hold for shape identification. We demonstrated that aging results in a reduction in the ability to visually recognize 3-D shape independent of how the 3-D structure is defined (motions of isolated points, deformations of smooth optical fields containing specular highlights, etc.).

AMI: Augmented Michelson Interferometer

NASA Astrophysics Data System (ADS)

Furió, David; Hachet, Martin; Guillet, Jean-Paul; Bousquet, Bruno; Fleck, Stéphanie; Reuter, Patrick; Canioni, Lionel

2015-10-01

Experiments in optics are essential for learning and understanding physical phenomena. The problem with these experiments is that they are generally time consuming for both their construction and their maintenance, potentially dangerous through the use of laser sources, and often expensive due to high technology optical components. We propose to simulate such experiments by way of hybrid systems that exploit both spatial augmented reality and tangible interaction. In particular, we focus on one of the most popular optical experiments: the Michelson interferometer. In our approach, we target a highly interactive system where students are able to interact in real time with the Augmented Michelson Interferometer (AMI) to observe, test hypotheses and then to enhance their comprehension. Compared to a fully digital simulation, we are investigating an approach that benefits from both physical and virtual elements, and where the students experiment by manipulating 3D-printed physical replicas of optical components (e.g. lenses and mirrors). Our objective is twofold. First, we want to ensure that the students will learn with our simulator the same concepts and skills that they learn with traditional methods. Second, we hypothesis that such a system opens new opportunities to teach optics in a way that was not possible before, by manipulating concepts beyond the limits of observable physical phenomena. To reach this goal, we have built a complementary team composed of experts in the field of optics, human-computer interaction, computer graphics, sensors and actuators, and education science.

Optical subcarrier processing for Nyquist SCM signals via coherent spectrum overlapping in four-wave mixing with coherent multi-tone pump.

PubMed

Lu, Guo-Wei; Luís, Ruben S; Mendinueta, José Manuel Delgado; Sakamoto, Takahide; Yamamoto, Naokatsu

2018-01-22

As one of the promising multiplexing and multicarrier modulation technologies, Nyquist subcarrier multiplexing (Nyquist SCM) has recently attracted research attention to realize ultra-fast and ultra-spectral-efficient optical networks. In this paper, we propose and experimentally demonstrate optical subcarrier processing technologies for Nyquist SCM signals such as frequency conversion, multicast and data aggregation of subcarriers, through the coherent spectrum overlapping between subcarriers in four-wave mixing (FWM) with coherent multi-tone pump. The data aggregation is realized by coherently superposing or combining low-level subcarriers to yield high-level subcarriers in the optical field. Moreover, multiple replicas of the data-aggregated subcarriers and the subcarriers carrying the original data are obtained. In the experiment, two 5 Gbps quadrature phase-shift keying (QPSK) subcarriers are coherently combined to generate a 10 Gbps 16 quadrature amplitude modulation (QAM) subcarrier with frequency conversions through the FWM with coherent multi-tone pump. Less than 1 dB optical signal-to-noise ratio (OSNR) penalty variation is observed for the synthesized 16QAM subcarriers after the data aggregation. In addition, some subcarriers are kept in the original formats, QPSK, with a power penalty of less than 0.4 dB with respect to the original input subcarriers. The proposed subcarrier processing technology enables flexibility for spectral management in future dynamic optical networks.

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.

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.

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.

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.

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.

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.

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.

Colloids exposed to random potential energy landscapes: From particle number density to particle-potential and particle-particle interactions

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

Bewerunge, Jörg; Capellmann, Ronja F.; Platten, Florian

2016-07-28

Colloidal particles were exposed to a random potential energy landscape that has been created optically via a speckle pattern. The mean particle density as well as the potential roughness, i.e., the disorder strength, were varied. The local probability density of the particles as well as its main characteristics were determined. For the first time, the disorder-averaged pair density correlation function g{sup (1)}(r) and an analogue of the Edwards-Anderson order parameter g{sup (2)}(r), which quantifies the correlation of the mean local density among disorder realisations, were measured experimentally and shown to be consistent with replica liquid state theory results.

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.

3-D profilometer using a CCD linear image sensor: application to skin surface topography measurement.

PubMed

Nita, D; Mignot, J; Chuard, M; Sofa, M

1998-08-01

Measurement of cutaneous surface topography can be made by three-dimensional (3-D) profilometry. Different equipment is used for this measurement. The magnitude of the vertical scale required, which can vary from several tens of micrometers (microrelief) to several millimeters (skin pathologies), depends also on the precision required and the duration of acquisition time. Over the last few years, different apparatuses have been produced, with a vertical range that is most frequently used for classical industrial applications, i.e., 0-1000 μm. The system developed here has a wide range of about 7 mm and is accurate enough to analyse each of the different skin surfaces that fall in this range without changing magnification. An optical principle, operating without any contact with a skin replica, allows a precise measurement with a high scanning speed. The profilometer has a vertical sensitivity of 4 μm within a vertical range of 7 mm. This sensitivity is lower than that of a mechanical or focusing profilometer, but the vertical range is wider. The system has several advantages: because of its verticale range, it can measure large surfaces with great roughness variations; the initial position of the replica beneath the profilometer must be within the 7 mm vertical range; and skin topography can be quantified, without contact, in a short time.

Straightforward and precise approach to replicate complex hierarchical structures from plant surfaces onto soft matter polymer

PubMed Central

Speck, Thomas; Bohn, Holger F.

2018-01-01

The surfaces of plant leaves are rarely smooth and often possess a species-specific micro- and/or nano-structuring. These structures usually influence the surface functionality of the leaves such as wettability, optical properties, friction and adhesion in insect–plant interactions. This work presents a simple, convenient, inexpensive and precise two-step micro-replication technique to transfer surface microstructures of plant leaves onto highly transparent soft polymer material. Leaves of three different plants with variable size (0.5–100 µm), shape and complexity (hierarchical levels) of their surface microstructures were selected as model bio-templates. A thermoset epoxy resin was used at ambient conditions to produce negative moulds directly from fresh plant leaves. An alkaline chemical treatment was established to remove the entirety of the leaf material from the cured negative epoxy mould when necessary, i.e. for highly complex hierarchical structures. Obtained moulds were filled up afterwards with low viscosity silicone elastomer (PDMS) to obtain positive surface replicas. Comparative scanning electron microscopy investigations (original plant leaves and replicated polymeric surfaces) reveal the high precision and versatility of this replication technique. This technique has promising future application for the development of bioinspired functional surfaces. Additionally, the fabricated polymer replicas provide a model to systematically investigate the structural key points of surface functionalities. PMID:29765666

Surface modification using the biomimetic method in alumina-zirconia porous ceramics obtained by the replica method.

PubMed

Silva, André D R; Rigoli, Willian R; Osiro, Denise; Mello, Daphne C R; Vasconcellos, Luana M R; Lobo, Anderson O; Pallone, Eliria M J A

2018-01-12

The modification of biomaterials approved by the Food and Drug Administration could be an alternative to reduce the period of use in humans. Porous bioceramics are widely used as support structures for bone formation and repair. This composite has essential characteristics for an implant, including good mechanical properties, high chemical stability, biocompatibility and adequate aesthetic appearance. Here, three-dimensional porous scaffolds of Al 2 O 3 containing 5% by volume of ZrO 2 were produced by the replica method. These scaffolds had their surfaces chemically treated with phosphoric acid and were coated with calcium phosphate using the biomimetic method simulated body fluid (SBF, 5×) for 14 days. The scaffolds, before and after biomimetic coating, were characterized mechanically, morphologically and structurally by axial compression tests, scanning electron microscopy, microtomography, apparent porosity, X-ray diffractometry, near-infrared spectroscopy, inductively coupled plasma optical emission spectroscopy, energy dispersive X-ray spectroscopy and reactivity. The in vitro cell viability and formation of mineralization nodules were used to identify the potential for bone regeneration. The produced scaffols after immersion in SBF were able to induce the nodules formation. These characteristics are advantaged by the formation of different phases of calcium phosphates on the material surface in a reduced incubation period. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2018. © 2018 Wiley Periodicals, Inc.

Evaluation of Two Protocols to Measure the Accuracy of Fixed Dental Prostheses: An In Vitro Study.

PubMed

Schönberger, Joana; Erdelt, Kurt-Jürgen; Bäumer, Daniel; Beuer, Florian

2017-02-02

The aim of this in vitro study was to compare two measurement protocols of the internal and marginal fit of three-unit zirconia fixed dental prostheses (FDPs). Forty-four FDPs were fabricated for standardized dies by two laboratory CAD/CAM systems: Cercon (n = 22) and Ceramill (n = 22). The fitting was tested using a replica technique (RT = technique 1) with a light-body silicone stabilized with heavy-body material. After producing the replicas, cross-sections were made in the buccolingual and mesiodistal directions. FDPs were cemented on definitive dies, embedded, and sectioned (CST = technique 2). The marginal and internal fits were measured under an optical microscope at 50x magnification with a special software program. Data evaluation was performed according to prior studies at a level of significance of 5%. The mean internal gap width was 51 ± 36 μm for the RT and 52 ± 35 μm for the cross-section technique (CST) (p = 0.74). The mean marginal gap width was 27 ± 18 μm for RT and 30 ± 19 μm for CST (p = 0.19). Statistical tests showed no significant differences (p > 0.05). Both techniques can be used for fit evaluation; however, the noninvasive RT is suitable for clinical use. © 2017 by the American College of Prosthodontists.

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.

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…

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.

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.

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.

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.

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.

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.

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.

Femtosecond to picosecond transient effects in WSe 2 observed by pump-probe angle-resolved photoemission spectroscopy.

PubMed

Liu, Ro-Ya; Ogawa, Yu; Chen, Peng; Ozawa, Kenichi; Suzuki, Takeshi; Okada, Masaru; Someya, Takashi; Ishida, Yukiaki; Okazaki, Kozo; Shin, Shik; Chiang, Tai-Chang; Matsuda, Iwao

2017-11-22

Time-dependent responses of materials to an ultrashort optical pulse carry valuable information about the electronic and lattice dynamics; this research area has been widely studied on novel two-dimensional materials such as graphene, transition metal dichalcogenides (TMDs) and topological insulators (TIs). We report herein a time-resolved and angle-resolved photoemission spectroscopy (TRARPES) study of WSe 2 , a layered semiconductor of interest for valley electronics. The results for below-gap optical pumping reveal energy-gain and -loss Floquet replica valence bands that appear instantaneously in concert with the pump pulse. Energy shift, broadening, and complex intensity variation and oscillation at twice the phonon frequency for the valence bands are observed at time scales ranging from the femtosecond to the picosecond and beyond. The underlying physics is rich, including ponderomotive interaction, dressing of the electronic states, creation of coherent phonon pairs, and diffusion of charge carriers - effects operating at vastly different time domains.

Utilizing laser interference lithography to fabricate hierarchical optical active nanostructures inspired by the blue Morpho butterfly

NASA Astrophysics Data System (ADS)

Siddique, Radwanul H.; Faisal, Abrar; Hünig, Ruben; Bartels, Carolin; Wacker, Irene; Lemmer, Uli; Hoelscher, Hendrik

2014-09-01

The famous non-iridescent blue of the Morpho butter by is caused by a `Christmas tree' like nanostructure which is a challenge for common fabrication techniques. Here, we introduce a method to fabricate this complex morphology utilizing dual beam interference lithography. We add a reflective coating below the photoresist to create a second interference pattern in vertical direction by exploiting the back reflection from the substrate. This vertical pattern exposes the lamella structure into the photosensitive polymer while the horizontal interference pattern determines the distance of the ridges. The photosensitive polymer is chosen accordingly to create the Christmas tree' like tapered shape. The resulting artificial Morpho replica shows brilliant non-iridescent blue up to an incident angle of 40. Its optical properties are close to the original Morpho structure because the refractive index of the polymer is close to chitin. Moreover, the biomimetic surface is water repellent with a contact angle of 110.

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.

Development of nanoimprint lithography templates for the contact hole layer application (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ichimura, Koji; Hikichi, Ryugo; Harada, Saburo; Kanno, Koichi; Kurihara, Masaaki; Hayashi, Naoya

2017-04-01

Nanoimprint lithography, NIL, is gathering much attention as one of the most potential candidates for the next generation lithography for semiconductor. This technology needs no pattern data modification for exposure, simpler exposure system, and single step patterning process without any coat/develop truck, and has potential of cost effective patterning rather than very complex optical lithography and/or EUV lithography. NIL working templates are made by the replication of the EB written high quality master templates. Fabrication of high resolution master templates is one of the most important issues. Since NIL is 1:1 pattern transfer process, master templates have 4 times higher resolution compared with photomasks. Another key is to maintain the quality of the master templates in replication process. NIL process is applied for the template replication and this imprint process determines most of the performance of the replicated templates. Expectations to the NIL are not only high resolution line and spaces but also the contact hole layer application. Conventional ArF-i lithography has a certain limit in size and pitch for contact hole fabrication. On the other hand, NIL has good pattern fidelity for contact hole fabrication at smaller sizes and pitches compared with conventional optical lithography. Regarding the tone of the templates for contact hole, there are the possibilities of both tone, the hole template and the pillar template, depending on the processes of the wafer side. We have succeeded to fabricate both types of templates at 2xnm in size. In this presentation, we will be discussing fabrication or our replica template for the contact hole layer application. Both tone of the template fabrication will be presented as well as the performance of the replica templates. We will also discuss the resolution improvement of the hole master templates by using various e-beam exposure technologies.

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.

Monte Carlo simulations of adult and pediatric computed tomography exams: Validation studies of organ doses with physical phantoms

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

Long, Daniel J.; Lee, Choonsik; Tien, Christopher

2013-01-15

Purpose: To validate the accuracy of a Monte Carlo source model of the Siemens SOMATOM Sensation 16 CT scanner using organ doses measured in physical anthropomorphic phantoms. Methods: The x-ray output of the Siemens SOMATOM Sensation 16 multidetector CT scanner was simulated within the Monte Carlo radiation transport code, MCNPX version 2.6. The resulting source model was able to perform various simulated axial and helical computed tomographic (CT) scans of varying scan parameters, including beam energy, filtration, pitch, and beam collimation. Two custom-built anthropomorphic phantoms were used to take dose measurements on the CT scanner: an adult male and amore » 9-month-old. The adult male is a physical replica of University of Florida reference adult male hybrid computational phantom, while the 9-month-old is a replica of University of Florida Series B 9-month-old voxel computational phantom. Each phantom underwent a series of axial and helical CT scans, during which organ doses were measured using fiber-optic coupled plastic scintillator dosimeters developed at University of Florida. The physical setup was reproduced and simulated in MCNPX using the CT source model and the computational phantoms upon which the anthropomorphic phantoms were constructed. Average organ doses were then calculated based upon these MCNPX results. Results: For all CT scans, good agreement was seen between measured and simulated organ doses. For the adult male, the percent differences were within 16% for axial scans, and within 18% for helical scans. For the 9-month-old, the percent differences were all within 15% for both the axial and helical scans. These results are comparable to previously published validation studies using GE scanners and commercially available anthropomorphic phantoms. Conclusions: Overall results of this study show that the Monte Carlo source model can be used to accurately and reliably calculate organ doses for patients undergoing a variety of axial or helical CT examinations on the Siemens SOMATOM Sensation 16 scanner.« less

Inspection, 3D modelling, and rapid prototyping of cultural heritage by means of a 3D optical digitiser

NASA Astrophysics Data System (ADS)

Docchio, F.; Sansoni, G.; Trebeschi, M.

2005-06-01

This paper presents the activity carried out to perform the three-dimensional acquisition of the "Vittoria Alata", a 2m-high, bronze statue, symbol of our City, located at the Civici Musei di Arte e Storia (S. Giulia) of Brescia. The acquisition of the statue has been performed by using a three-dimensional vision system based on active triangulation and on the projection of non-coherent light. This system, called OPL-3D, represents one of the research products of our Laboratory, which has been active for years in the development of techniques and systems for the contactless acquisition of free-form, complex shapes. The study, originally motivated by the need to explore a new hypothesis on the origin of the "Vittoria Alata", led to its complete digitization and description in terms of both polygonal and NURBS-based models. A suite of copies of the whole statue has been obtained in the framework of the collaboration between the City Museum and the EOS Electro Optical Systems GmbH, located in Munich, Germany. As a first step, one 30 cm-high replica of the whole statue has been produced using a low-resolution triangle model of the statue (3.5 millions of triangles). As a second step, two 1:1 scale copies of the statue have been produced. For them, the Laboratory has provided the high resolution STL file (16 millions of triangles). The paper discusses in detail the hardware and the software facilities used to implement the whole process, and gives a comprehensive description of the results.

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.

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.

Tailoring the nature and strength of electron-phonon interactions in the SrTiO3(001) 2D electron liquid

NASA Astrophysics Data System (ADS)

Wang, Z.; McKeown Walker, S.; Tamai, A.; Wang, Y.; Ristic, Z.; Bruno, F. Y.; de la Torre, A.; Riccò, S.; Plumb, N. C.; Shi, M.; Hlawenka, P.; Sánchez-Barriga, J.; Varykhalov, A.; Kim, T. K.; Hoesch, M.; King, P. D. C.; Meevasana, W.; Diebold, U.; Mesot, J.; Moritz, B.; Devereaux, T. P.; Radovic, M.; Baumberger, F.

2016-08-01

Surfaces and interfaces offer new possibilities for tailoring the many-body interactions that dominate the electrical and thermal properties of transition metal oxides. Here, we use the prototypical two-dimensional electron liquid (2DEL) at the SrTiO3(001) surface to reveal a remarkably complex evolution of electron-phonon coupling with the tunable carrier density of this system. At low density, where superconductivity is found in the analogous 2DEL at the LaAlO3/SrTiO3 interface, our angle-resolved photoemission data show replica bands separated by 100 meV from the main bands. This is a hallmark of a coherent polaronic liquid and implies long-range coupling to a single longitudinal optical phonon branch. In the overdoped regime the preferential coupling to this branch decreases and the 2DEL undergoes a crossover to a more conventional metallic state with weaker short-range electron-phonon interaction. These results place constraints on the theoretical description of superconductivity and allow a unified understanding of the transport properties in SrTiO3-based 2DELs.

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.

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

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.

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.

Optoelectronic associative memory

NASA Technical Reports Server (NTRS)

Chao, Tien-Hsin (Inventor)

1993-01-01

An associative optical memory including an input spatial light modulator (SLM) in the form of an edge enhanced liquid crystal light valve (LCLV) and a pair of memory SLM's in the form of liquid crystal televisions (LCTV's) forms a matrix array of an input image which is cross correlated with a matrix array of stored images. The correlation product is detected and nonlinearly amplified to illuminate a replica of the stored image array to select the stored image correlating with the input image. The LCLV is edge enhanced by reducing the bias frequency and voltage and rotating its orientation. The edge enhancement and nonlinearity of the photodetection improves the orthogonality of the stored image. The illumination of the replicate stored image provides a clean stored image, uncontaminated by the image comparison process.

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.

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.

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

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.

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.

Corrosion investigation of fire-gilded bronze involving high surface resolution spectroscopic imaging

NASA Astrophysics Data System (ADS)

Masi, G.; Chiavari, C.; Avila, J.; Esvan, J.; Raffo, S.; Bignozzi, M. C.; Asensio, M. C.; Robbiola, L.; Martini, C.

2016-03-01

Gilded bronzes are often affected by severe corrosion, due to defects in the Au layer and Au/Cu alloy galvanic coupling, stimulated by large cathodic area of the gilded layer. Galvanic corrosion, triggered by gilding defects, leads to products growth at the Au/bronze interface, inducing blistering or break-up of the Au layer. In this context, fire-gilded bronze replicas prepared by ancient methods (use of spreadable Au-Hg paste) was specifically characterised by compiling complementary spectroscopic and imaging information before/after accelerated ageing with synthetic rain. Fire-gilded bronze samples were chemically imaged in cross-section at nano-metric scale (<200 nm) using high energy and lateral resolution synchrotron radiation photoemission (HR-SRPES) of core levels and valence band after conventional characterisation of the samples by Glow Discharge optical Emission Spectroscopy (GD-OES) and conventional X-ray photoelectron spectroscopy (XPS). We have found a net surface enrichment in Zn and Sn after fire-gilding and presence of metallic Hg, Pb and Cu within the Au layer. Moreover, the composition distribution of the elements together with their oxidation has been determined. It was also revealed that metallic phases including Hg and Pb remain in the gilding after corrosion. Moreover, selective dissolution of Zn and Cu occurs in the crater due to galvanic coupling, which locally induces relative Sn species enrichment (decuprification). The feasibility advantages and disadvantages of chemical imaging using HR-SRPES to study artworks have been investigated on representative replicas.

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

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

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.

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 ...

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

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.

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.

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.

Evaluation of a reproduction technique for the study of the enamel composite/bracket base area.

PubMed

Wilner, F J; Oliver, R G

2000-09-01

The objective of the study was to evaluate a reproduction method that would enable the study of the enamel/ bracket/composite interface in vivo, and consisted of in vitro assessment of two different impression materials to compare reproduction of brackets bonded to extracted teeth followed by in vivo assessment of the superior material. In vitro standard edgewise brackets were bonded to two extracted teeth and impressions were taken using two different types of low viscosity silicone-based impression materials. A medium viscosity silicone impression material was used to support the original impression. Three impressions of both the gingival and occlusal aspect of the bracket base region were obtained using each of the impression materials. Replicas were then prepared for SEM viewing and these compared to SEMs of the real teeth for reproduction of detail. A 3-point Reproducibility Index was used to compare the SEM photographs of the comparable replicas. One impression material was clearly superior to the other and produced an acceptably accurate representation of the true clinical situation in three out of four samples. This material also performed well in the in vivo situation. The technique described is satisfactory for the production and analysis of SEM pictures of the enamel/composite/ bracket base interface in vivo.

Helios: a tangible and augmented environment to learn optical phenomena in astronomy

NASA Astrophysics Data System (ADS)

Fleck, Stéphanie; Hachet, Martin

2015-10-01

France is among the few countries that have integrated astronomy in primary school levels. However, for fifteen years, a lot of studies have shown that children have difficulties in understanding elementary astronomic phenomena such as day/night alternation, seasons or moon phases' evolution. To understand these phenomena, learners have to mentally construct 3D perceptions of aster motions and to understand how light propagates from an allocentric point of view. Therefore, 4-5 grades children (8 to 11 years old), who are developing their spatial cognition, have many difficulties to assimilate geometric optical problems that are linked to astronomy. To make astronomical learning more efficient for young pupils, we have designed an Augmented Inquiry-Based Learning Environment (AIBLE): HELIOS. Because manipulations in astronomy are intrinsically not possible, we propose to manipulate the underlying model. With HELIOS, virtual replicas of the Sun, Moon and Earth are directly manipulated from tangible manipulations. This digital support combines the possibilities of Augmented Reality (AR) while maintaining intuitive interactions following the principles of didactic of sciences. Light properties are taken into account and shadows of Earth and Moon are directly produced by an omnidirectional light source associated to the virtual Sun. This AR environment provides users with experiences they would otherwise not be able to experiment in the physical world. Our main goal is that students can take active control of their learning, express and support their ideas, make predictions and hypotheses, and test them by conducting investigations.

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.

A programmable nanoreplica molding for the fabrication of nanophotonic devices.

PubMed

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-03-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively.

A programmable nanoreplica molding for the fabrication of nanophotonic devices

PubMed Central

Liu, Longju; Zhang, Jingxiang; Badshah, Mohsin Ali; Dong, Liang; Li, Jingjing; Kim, Seok-min; Lu, Meng

2016-01-01

The ability to fabricate periodic structures with sub-wavelength features has a great potential for impact on integrated optics, optical sensors, and photovoltaic devices. Here, we report a programmable nanoreplica molding process to fabricate a variety of sub-micrometer periodic patterns using a single mold. The process utilizes a stretchable mold to produce the desired periodic structure in a photopolymer on glass or plastic substrates. During the replica molding process, a uniaxial force is applied to the mold and results in changes of the periodic structure, which resides on the surface of the mold. Direction and magnitude of the force determine the array geometry, including the lattice constant and arrangement. By stretching the mold, 2D arrays with square, rectangular, and triangular lattice structures can be fabricated. As one example, we present a plasmonic crystal device with surface plasmon resonances determined by the force applied during molding. In addition, photonic crystal slabs with different array patterns are fabricated and characterized. This unique process offers the capability of generating various periodic nanostructures rapidly and inexpensively. PMID:26925828

Optical study of the band structure of wurtzite GaP nanowires

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

Assali, S., E-mail: simone.assali@polymtl.ca; Greil, J.; Zardo, I.

2016-07-28

We investigated the optical properties of wurtzite (WZ) GaP nanowires by performing photoluminescence (PL) and time-resolved PL measurements in the temperature range from 4 K to 300 K, together with atom probe tomography to identify residual impurities in the nanowires. At low temperature, the WZ GaP luminescence shows donor-acceptor pair emission at 2.115 eV and 2.088 eV, and Burstein-Moss band-filling continuum between 2.180 and 2.253 eV, resulting in a direct band gap above 2.170 eV. Sharp exciton α-β-γ lines are observed at 2.140–2.164–2.252 eV, respectively, showing clear differences in lifetime, presence of phonon replicas, and temperature-dependence. The excitonic nature of those peaks is critically discussed, leading tomore » a direct band gap of ∼2.190 eV and to a resonant state associated with the γ-line ∼80 meV above the Γ{sub 8C} conduction band edge.« less

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

Iblisdir, S.; Gisin, N.; Acin, A.

We investigate the optimal distribution of quantum information over multipartite systems in asymmetric settings. We introduce cloning transformations that take N identical replicas of a pure state in any dimension as input and yield a collection of clones with nonidentical fidelities. As an example, if the clones are partitioned into a set of M{sub A} clones with fidelity F{sup A} and another set of M{sub B} clones with fidelity F{sup B}, the trade-off between these fidelities is analyzed, and particular cases of optimal N{yields}M{sub A}+M{sub B} cloning machines are exhibited. We also present an optimal 1{yields}1+1+1 cloning machine, which ismore » an example of a tripartite fully asymmetric cloner. Finally, it is shown how these cloning machines can be optically realized.« less

Use of fractography and sectioning techniques to study fracture mechanisms

NASA Technical Reports Server (NTRS)

Van Stone, R. H.; Cox, T. B.

1976-01-01

Recent investigations of the effect of microstructure on the fracture mechanisms and fracture toughness of steels, aluminum alloys, and titanium alloys have used standard fractographic techniques and a sectioning technique on specimens plastically deformed to various strains up to fracture. The specimens are prepared metallographically for observation in both optical and electron beam instruments. This permits observations to be made about the fracture mechanism as it occurs in thick sections and helps remove speculation from the interpretation of fractographic features. This technique may be used in conjunction with other standard techniques such as extraction replicas and microprobe analyses. Care must be taken to make sure that the microstructural features which are observed to play a role in the fracture process using the sectioning technique can be identified with fractography.

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…

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

Precision glass molding of high-resolution diffractive optical elements

NASA Astrophysics Data System (ADS)

Prater, Karin; Dukwen, Julia; Scharf, Toralf; Herzig, Hans P.; Plöger, Sven; Hermerschmidt, Andreas

2016-04-01

The demand of high resolution diffractive optical elements (DOE) is growing. Smaller critical dimensions allow higher deflection angles and can fulfill more demanding requirements, which can only be met by using electron-beam lithography. Replication techniques are more economical, since the high cost of the master can be distributed among a larger number of replicas. The lack of a suitable mold material for precision glass molding has so far prevented an industrial use. Glassy Carbon (GC) offers a high mechanical strength and high thermal strength. No anti-adhesion coatings are required in molding processes. This is clearly an advantage for high resolution, high aspect ratio microstructures, where a coating with a thickness between 10 nm and 200 nm would cause a noticeable rounding of the features. Electron-beam lithography was used to fabricate GC molds with highest precision and feature sizes from 250 nm to 2 μm. The master stamps were used for precision glass molding of a low Tg glass L-BAL42 from OHARA. The profile of the replicated glass is compared to the mold with the help of SEM images. This allows discussion of the max. aspect-ratio and min. feature size. To characterize optical performances, beamsplitting elements are fabricated and their characteristics were investigated, which are in excellent agreement to theory.

A development roadmap for critical technologies needed for TALC: a deployable 20m annular space telescope

NASA Astrophysics Data System (ADS)

Sauvage, Marc; Amiaux, Jérome; Austin, James; Bello, Mara; Bianucci, Giovanni; Chesné, Simon; Citterio, Oberto; Collette, Christophe; Correia, Sébastien; Durand, Gilles A.; Molinari, Sergio; Pareschi, Giovanni; Penfornis, Yann; Sironi, Giorgia; Valsecchi, Giuseppe; Verpoort, Sven; Wittrock, Ulrich

2016-07-01

Astronomy is driven by the quest for higher sensitivity and improved angular resolution in order to detect fainter or smaller objects. The far-infrared to submillimeter domain is a unique probe of the cold and obscured Universe, harboring for instance the precious signatures of key elements such as water. Space observations are mandatory given the blocking effect of our atmosphere. However the methods we have relied on so far to develop increasingly larger telescopes are now reaching a hard limit, with the JWST illustrating this in more than one way (e.g. it will be launched by one of the most powerful rocket, it requires the largest existing facility on Earth to be qualified). With the Thinned Aperture Light Collector (TALC) project, a concept of a deployable 20 m annular telescope, we propose to break out of this deadlock by developing novel technologies for space telescopes, which are disruptive in three aspects: • An innovative deployable mirror whose topology, based on stacking rather than folding, leads to an optimum ratio of collecting area over volume, and creates a telescope with an eight times larger collecting area and three times higher angular resolution compared to JWST from the same pre-deployed volume; • An ultra-light weight segmented primary mirror, based on electrodeposited Nickel, Composite and Honeycomb stacks, built with a replica process to control costs and mitigate the industrial risks; • An active optics control layer based on piezo-electric layers incorporated into the mirror rear shell allowing control of the shape by internal stress rather than by reaction on a structure. We present in this paper the roadmap we have built to bring these three disruptive technologies to technology readiness level 3. We will achieve this goal through design and realization of representative elements: segments of mirrors for optical quality verification, active optics implemented on representative mirror stacks to characterize the shape correction capabilities, and mechanical models for validation of the deployment concept. Accompanying these developments, a strong system activity will ensure that the ultimate goal of having an integrated system can be met, especially in terms of (a) scalability toward a larger structure, and (b) verification philosophy.

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.

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

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.

Novel nanoplasmonic biosensor integrated in a microfluidic channel

NASA Astrophysics Data System (ADS)

Solis-Tinoco, V.; Sepulveda, B.; Lechuga, L. M.

2015-06-01

An important motivation of the actual biosensor research is to develop a multiplexed sensing platform of high sensitivity fabricated with large-scale and low-cost technologies for applications such as diagnosis and monitoring of diseases, drug discovery and environmental control. Biosensors based on localized plasmon resonance (LSPR) have demonstrated to be a novel and effective platform for quantitative detection of biological and chemical analytes. Here, we describe a novel label-free nanobiosensor consisting of an array of closely spaced, vertical, elastomeric nanopillars capped with plasmonic gold nanodisks in a SU-8 channel. The principle is based on the refractive index sensing using the LSPR of gold nanodisks. The fabrication of the nanobiosensor is based on replica molding technique and gold nanodisks are incorporated on the polymer structures by e-beam evaporation. In this work, we provide the strategies for controlling the silicon nanostructure replication using thermal polymers and photopolymers with different Young's modulus, in order to minimize the common distortions in the process and to obtain a reliable replica of the Si master. The master mold of the biosensor consists of a hexagonal array of silicon nanopillars, whose diameter is ~200 nm, and whose height can range from 250 nm to 1.300 μm, separated 400 nm from the center to center, integrated in a SU-8 microfluidic channel.

Fabrication of microlens array and bifocal microlens using the methods of laser ablation and solvent reflow

NASA Astrophysics Data System (ADS)

Yu, Cheng-Chian; Ho, Jeng-Rong

2015-12-01

Based on the techniques of laser microdrilling and solvent reflow, this study reports on a straightforward approach for fabricating plastic microlens arrays (MLAs). First, we use the ArF excimer laser to drill microholes on a polymethylmethacrylate plate for defining the lens number, initial depth, and diameter. The propylene glycol monomethyl ether acetate solvent is then employed to regulate the surface profile that leads to a resulting negative (concave) MLA. The corresponding positive (convex), polydimethyl-siloxane MLA is obtained by the soft-replica-molding technique. Through varying the pattern size and period on the mask and the light intensity for laser drilling and regulating the solvent in the reflow process, we exhibit the feasibility of making MLAs with various sizes and shapes. By modifying the laser ablation step to drill two microholes with different diameters and depths at two levels, we fabricate a bifocal microlens. The obtained microlenses have excellent surface and optical properties: surface roughness down to several nanometers and focal lengths varying from hundreds to thousands of micrometers. This approach is flexible for constructing microlenses with various sizes and shapes and can fabricate MLAs with a high fill factor.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

Quantum Glass of Interacting Bosons with Off-Diagonal Disorder

NASA Astrophysics Data System (ADS)

Piekarska, A. M.; Kopeć, T. K.

2018-04-01

We study disordered interacting bosons described by the Bose-Hubbard model with Gaussian-distributed random tunneling amplitudes. It is shown that the off-diagonal disorder induces a spin-glass-like ground state, characterized by randomly frozen quantum-mechanical U(1) phases of bosons. To access criticality, we employ the "n -replica trick," as in the spin-glass theory, and the Trotter-Suzuki method for decomposition of the statistical density operator, along with numerical calculations. The interplay between disorder, quantum, and thermal fluctuations leads to phase diagrams exhibiting a glassy state of bosons, which are studied as a function of model parameters. The considered system may be relevant for quantum simulators of optical-lattice bosons, where the randomness can be introduced in a controlled way. The latter is supported by a proposition of experimental realization of the system in question.

Hard X-Ray and Wide Focusing Telescopes

NASA Technical Reports Server (NTRS)

Gorenstein, Paul

1998-01-01

Studies are being carried out to compare the performance of several different separation materials used in the replication process. This report presents the results obtained during the second year of a program which consists of replicating smooth, thin substrates, depositing multilayer coatings upon them, and evaluating their performance. Replication and multilayer coatings are both critically important to the development of focussing hard X-ray telescopes that function up to 100 keV. The activities of the current year include extending the comparison between sputtered amorphous carbon and evaporated gold to include sputtered as well as evaporated gold. The figure of merit being the smoothness of the replica which has a direct effect on the specular reflectivity. These results were obtained with epoxy replication, but they should be applicable to electroformed nickel, the process we expect to use for the ultimate replicated optics.

Synthesis of metal nanoparticle and patterning in polymeric films induced by electron beam

NASA Astrophysics Data System (ADS)

Yamamoto, Hiroki; Kozawa, Takahiro; Tagawa, Seiichi; Marignier, Jean-Louis; Mostafavi, Mehran; Belloni, Jacqueline

2018-03-01

Using an electron beam, thin polymeric films loaded with metal nanoparticles of silver were prepared by a one-step irradiation-induced reduction of the metal ions embedded in the polymer. The metal nanoparticles were observed by either optical absorption or microscopy. The mechanism of the reduction of metal ions and of the polymer crosslinking were deduced from the average absorbance measurements. In view of realizing specific patterns of high resolution using the electron beam, electron beam produces 200 nm wide lines that can be separated by unexposed spaces of adjustable width, where precursors were dissolved. The resolution of the electron beam has been exploited to demonstrate the achievement of nanopatterning on polymer films using a direct-writing process. This method supplies interesting applications such as masks, replicas, or imprint molds of improved density and contrast.

On the luminescence of freshly introduced a-screw dislocations in low-resistance GaN

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

Medvedev, O. S., E-mail: o.s.medvedev@spbu.ru; Vyvenko, O. F.; Bondarenko, A. S.

2015-09-15

Using scanning electron microscopy in the cathodoluminescence mode, it is shown that straight segments of a-screw dislocations introduced by plastic deformation at room temperature into unintentionally doped low-resistance gallium nitride luminesce in the spectral range 3.1–3.2 eV at 70 K. The spectral composition of dislocation luminescence shows a fine doublet structure with a component width of ∼15 meV and splitting of ∼30 meV, accompanied by LO-phonon replicas. Luminescent screw dislocations move upon exposure to an electron beam and at low temperatures, but retain immobility for a long time without external excitation. Optical transitions involving the quantum-well states of a stackingmore » fault in a split-dislocation core are considered to be the most probable mechanism of the observed phenomenon.« less

High resolution Fourier transform spectroscopy and crystal-field analysis in Tm,Ho:BaY2F8

NASA Astrophysics Data System (ADS)

Baraldi, A.; Capelletti, R.; Mazzera, M.; Riolo, P.; Amoretti, G.; Magnani, N.; Sani, E.; Toncelli, A.; Tonelli, M.

2005-01-01

A Tm3+- Ho3+ -codoped single crystal of monoclinic BaY2F8 has been characterized by means of high resolution FTIR spectroscopy in the wave number range 2000-24000 cm-1 and in the temperature range 9-300 K. The energy level schemes of the two lanthanide ions as determined by the optical absorption spectra is presented, analyzed, and fitted within a single ion Hamiltonian model. The very small energy separation (about 0.6-1.6 cm-1) measured between the first and second sublevels of the ground state manifolds for both the ions is in line with the theoretical predictions. The impurity-phonon coupling is put into evidence by the thermally induced line shift and broadening, and by the detection of vibronic replicas of a few lines.

Highly stretchable electroluminescent skin for optical signaling and tactile sensing.

PubMed

Larson, C; Peele, B; Li, S; Robinson, S; Totaro, M; Beccai, L; Mazzolai, B; Shepherd, R

2016-03-04

Cephalopods such as octopuses have a combination of a stretchable skin and color-tuning organs to control both posture and color for visual communication and disguise. We present an electroluminescent material that is capable of large uniaxial stretching and surface area changes while actively emitting light. Layers of transparent hydrogel electrodes sandwich a ZnS phosphor-doped dielectric elastomer layer, creating thin rubber sheets that change illuminance and capacitance under deformation. Arrays of individually controllable pixels in thin rubber sheets were fabricated using replica molding and were subjected to stretching, folding, and rolling to demonstrate their use as stretchable displays. These sheets were then integrated into the skin of a soft robot, providing it with dynamic coloration and sensory feedback from external and internal stimuli. Copyright © 2016, American Association for the Advancement of Science.

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.

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.

Phonon coupling in optical transitions for singlet-triplet pairs of bound excitons in semiconductors

NASA Astrophysics Data System (ADS)

Pistol, M. E.; Monemar, B.

1986-05-01

A model is presented for the observed strong difference in selection rules for coupling of phonons in the one-phonon sideband of optical spectra related to bound excitons in semiconductors. The present treatment is specialized to the case of a closely spaced pair of singlet-triplet character as the lowest electronic states, as is common for bound excitons associated with neutral complexes in materials like GaP and Si. The optical transition for the singlet bound-exciton state is found to couple strongly only to symmetric A1 modes. The triplet state has a similar coupling strength to A1 modes, but in addition strong contributions are found for replicas corresponding to high-density-of-states phonons TAX, LAX, and TOX. This can be explained by a treatment of particle-phonon coupling beyond the ordinary adiabatic approximation. A weak mixing between the singlet and triplet states is mediated by the phonon coupling, as described in first-order perturbation theory. The model derived in this work, for such phonon-induced mixing of closely spaced electronic states, is shown to explain the observed phonon coupling for several bound-exciton systems of singlet-triplet character in GaP. In addition, the observed oscillator strength of the forbidden triplet state may be explained as partly derived from phonon-induced mixing with the singlet state, which has a much larger oscillator strength.

Fabrication of anatomically tapered foveal pits for retinal phantoms for optical coherence tomography

NASA Astrophysics Data System (ADS)

Lee, Gary C. F.; Smith, Gennifer T.; Agrawal, Monica; Ellerbee, Audrey K.

2015-03-01

Optical Coherence Tomography (OCT) has become a standard tool for diagnosing retinal disease in many ophthalmology clinics. Nonetheless, the technical and clinical research communities still lack a standardized phantom that could aid in evaluating and normalizing the various scan protocols and OCT machines employed at different institutions. Existing retinal phantoms designed for OCT imaging mimic some important features of the retina, such as the thickness and scattering properties of its many layers. However, the morphology of the foveal pit and the visible tapering of the retinal layers underlying the surface surrounding the pit remains a challenge to replicate in current phantoms. Recent attempts at creating a realistic foveal pit include molding, ablation and laser etching but have not proved sufficient to replicate this particular anatomical feature. In this work, we demonstrate a new fabrication procedure that is capable of replicating the tapered appearance of the retinal layers near the foveal pit using a combination of spin-coating and replica molding. The ability to create an anatomically correct foveal pit will allow for a new phantom better suited for intra- and inter-system evaluation and for improved testing of retinal segmentation algorithms.

Blinking and spectral diffusion of CdSe/ZnS nanoparticles

NASA Astrophysics Data System (ADS)

Lorke, Axel; Braam, Daniel; Mölleken, Andreas; Offer, Matthias; Prinz, Günther; Geller, Martin

2012-02-01

Even though the tunable optical properties of colloidal nanoparticles have been studied extensively, their luminescent behaviour is still not fully understood. The random emission intermittency and the power-law of on- and off-times as well as shifts in the emission wavelength still lack a comprehensive understanding [1]. We investigate the excitonic structure of CdSe/ZnS core/shell nanoparticles using a micro-photoluminescence (PL) setup with confocal as well as imaging optics. The nanoparticles are dispersed in toluene with 1% PMMA and deposited by spin-coating on different substrates (bare Si/SiO2 as well as Si/SiO2 covered with different rough metallic layers). Depending on the substrate, we observe emission intermittency or nearly blinking-free emission with spectral jumps of 25 meV in the emission energy. Both can be assigned to excitonic transitions affected by additional charge inside or outside the nanoparticle [2]. Furthermore, we observe a phonon replica of 25 meV and smaller (<10 meV) energetic shifts of the emission lines, which are likely caused random charge variations in the environment of the nanoparticle. [4pt] [1] P. Frantsuzov et al., Nature 4, 519 (2008). [0pt] [2] A. Efros, Nature Mat. 7, 612 (2008)

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.

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

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

Enabling Super-Nyquist Wavefront Control on WFIRST

NASA Astrophysics Data System (ADS)

Bendek, Eduardo; Belikov, Ruslan; Sirbu, Dan; Shaklan, Stuart B.; Eldorado Riggs, A. J.

2018-01-01

A large fraction of sun-like stars is contained in Binary systems. Within 10pc there are 70 FGK stars from which, 43 belong to a multi-star system, and 28 of them have companion leak that is greater than 1e-9 contrast assuming typical Hubble-quality space optics. Currently, those binary stars are not included in the WFIRST-CGI target list, but they could be observed if high-contrast imaging around binary star systems using WFIRST is possible, increasing by 70% the number of possible FGK targets for the mission. The Multi-Star Wavefront Control (MSWC) algorithm can be used to suppress the companion star leakage. If the targets have angular separations larger than the Nyquist controllable region of the Deformable Mirror the MSWC must operate in its Super-Nyquist (SN) mode. This mode requires a target star replica within the SN region in order to provide the energy, and coherent light necessary to null speckles at SN angular separations. For the case of WFIRST, about half of the targets that can be observed using MSWC have angular separations larger than the Nyquist controllable region of the 48x48 actuator Deformable Mirror (DM) to be used. Here, we discuss multiple alternatives to generate those PSF replicas with minimal or no impact to the WFIRST Coronagraph instrument such as 1) the addition of a movable diffractive pupil mounted of the Shape Pupil wheel. 2) Design of a modified Shape Pupil design able to create a dark zone and at the same time diffract a small fraction of the starlight on the SN region. 3) Predict the minimum residual quilting on Xinetics DM that would allow observing a given target.

Heating of metallic implants and instruments induced by gradient switching in a 1.5-Tesla whole-body unit.

PubMed

Graf, Hansjörg; Steidle, Günter; Schick, Fritz

2007-11-01

To examine gradient switching-induced heating of metallic parts. Copper and titanium frames and sheets ( approximately 50 x 50 mm(2), 1.5 mm thick, frame width = 3 mm) surrounded by air were positioned in the scanner perpendicular to the static field horizontally 20 cm off-center. During the execution of a sequence (three-dimensional [3D] true fast imaging with steady precession [True-FISP], TR = 6.4 msec) exploiting the gradient capabilities (maximum gradient = 40 mT/m, maximum slew rate = 200 T/m/second), heating was measured with an infrared camera. Radio frequency (RF) amplitude was set to zero volts. Heating of a copper frame with a narrowing to 1 mm over 20 mm at one side was examined in air and in addition surrounded by several liters of gelled saline using fiber-optic thermography. Further heating studies were performed using an artificial hip made of titanium, and an aluminum replica of the hip prosthesis with the same geometry. For the copper specimens, considerable heating (>10 degrees C) in air and in gelled saline (>1.2 degrees C) could be observed. Heating of the titanium specimens was markedly less ( approximately 1 degrees C in air). For the titanium artificial hip no heating could be detected, while the rise in temperature for the aluminum replica was approximately 2.2 degrees C. Heating of more than 10 degrees C solely due to gradient switching without any RF irradiation was demonstrated in isolated copper wire frames. Under specific conditions (high gradient duty cycle, metallic loop of sufficient inductance and low resistance, power matching) gradient switching-induced heating of conductive specimens must be considered.

Observation of contrast agent response to chirp insonation with a simultaneous optical-acoustical system.

PubMed

Sun, Yang; Zhao, Shukui; Dayton, Paul A; Ferrara, Katherine W

2006-06-01

Rayleigh-Plesset analysis, ultra-high speed photography, and single bubble acoustical recordings previously were applied independently to characterize the radial oscillation and resulting echoes from a microbubble in response to an ultrasonic pulse. In addition, high-speed photography has shown that microbubbles are destroyed over a single pulse or pulse train by diffusion and fragmentation. In order to develop a single model to characterize microbubble echoes based on oscillatory and destructive characteristics, an optical-acoustical system was developed to simultaneously record the optical image and backscattered echo from each microbubble. Combined observation provides the opportunity to compare predictions for oscillation and echoes with experimental results and identify discrepancies due to diffusion or fragmentation. Optimization of agents and insonating pulse parameters may be facilitated with this system. The mean correlation of the predicted and experimental radius-time curves and echoes exceeds 0.7 for the parameters studied here. An important application of this new system is to record and analyze microbubble response to a long pulse in which diffusion is shown to occur over the pulse duration. The microbubble response to an increasing or decreasing chirp is evaluated using this new tool. For chirp insonation beginning with the lower center frequency, low-frequency modulation of the oscillation envelope was obvious. However, low-frequency modulation was not observed in the radial oscillation produced by decreasing chirp insonation. Comparison of the echoes from similar sized microbubbles following increasing and decreasing chirp insonation demonstrated that the echoes were not time-reversed replicas. Using a transmission pressure of 620 kPa, the -6 dB echo length was 0.9 and 1.1 micros for increasing and decreasing chirp insonation, respectively (P = 0.02). The mean power in the low-frequency portion of the echoes was 8 (mV)2 and 13 (mV)2 for increasing and decreasing chirp insonation, respectively (P = 0.01).

Observation of contrast agent response to chirp insonation with a simultaneous optical-acoustical system

PubMed Central

Sun, Yang; Zhao, Shukui; Dayton, Paul A.; Ferrara, Katherine W.

2006-01-01

Rayleigh-Plesset analysis, ultra-high speed photography, and single bubble acoustical recordings have previously been applied independently to characterize the radial oscillation and resulting echoes from a microbubble in response to an ultrasonic pulse. In addition, high speed photography has shown that microbubbles are destroyed over a single pulse or pulse train by diffusion and fragmentation. In order to develop a single model to characterize microbubble echoes based on oscillatory and destructive characteristics, an optical-acoustical system was developed to simultaneously record the optical image and backscattered echo from each microbubble. Combined observation provides the opportunity to compare predictions for oscillation and echoes with experimental results and identify discrepancies due to diffusion or fragmentation. Optimization of agents and insonating pulse parameters may be facilitated with this system. The mean correlation of the predicted and experimental radius-time curves and echoes exceeds 0.7 for the parameters studied here. An important application of this new system is to record and analyze microbubble response to a long pulse where diffusion is shown to occur over the pulse duration. The microbubble response to an increasing or decreasing chirp is evaluated using this new tool. For chirp insonation beginning with the lower center frequency, low frequency modulation of the oscillation envelope was obvious. However, low frequency modulation was not observed in the radial oscillation produced by decreasing chirp insonation. Comparison of the echoes from similar sized microbubbles following increasing and decreasing chirp insonation demonstrated that the echoes were not time-reversed replicas. Using a transmission pressure of 620 kPa, the −6 dB echo length was 0.9 and 1.1 μs for increasing and decreasing chirp insonation, respectively (P = 0.02). The mean power in the low frequency portion of the echoes was 8 (mV)2 and 13 (mV)2 for increasing and decreasing chirp insonation, respectively, (P = 0.01). PMID:16846145

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).

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.

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).

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.

Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange

DTIC Science & Technology

2010-01-01

formulations of molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage...ad hoc force term in the SGLD model. Introduction Molecular dynamics (MD) simulations of small proteins provide insight into the mechanisms and... molecular dynamics (MD) and Langevin dynamics (LD) simulations for the prediction of thermodynamic folding observables of the Trp-cage mini-protein. All

Preserving the Boltzmann ensemble in replica-exchange molecular dynamics.

PubMed

Cooke, Ben; Schmidler, Scott C

2008-10-28

We consider the convergence behavior of replica-exchange molecular dynamics (REMD) [Sugita and Okamoto, Chem. Phys. Lett. 314, 141 (1999)] based on properties of the numerical integrators in the underlying isothermal molecular dynamics (MD) simulations. We show that a variety of deterministic algorithms favored by molecular dynamics practitioners for constant-temperature simulation of biomolecules fail either to be measure invariant or irreducible, and are therefore not ergodic. We then show that REMD using these algorithms also fails to be ergodic. As a result, the entire configuration space may not be explored even in an infinitely long simulation, and the simulation may not converge to the desired equilibrium Boltzmann ensemble. Moreover, our analysis shows that for initial configurations with unfavorable energy, it may be impossible for the system to reach a region surrounding the minimum energy configuration. We demonstrate these failures of REMD algorithms for three small systems: a Gaussian distribution (simple harmonic oscillator dynamics), a bimodal mixture of Gaussians distribution, and the alanine dipeptide. Examination of the resulting phase plots and equilibrium configuration densities indicates significant errors in the ensemble generated by REMD simulation. We describe a simple modification to address these failures based on a stochastic hybrid Monte Carlo correction, and prove that this is ergodic.

Monte Carlo replica-exchange based ensemble docking of protein conformations.

PubMed

Zhang, Zhe; Ehmann, Uwe; Zacharias, Martin

2017-05-01

A replica-exchange Monte Carlo (REMC) ensemble docking approach has been developed that allows efficient exploration of protein-protein docking geometries. In addition to Monte Carlo steps in translation and orientation of binding partners, possible conformational changes upon binding are included based on Monte Carlo selection of protein conformations stored as ordered pregenerated conformational ensembles. The conformational ensembles of each binding partner protein were generated by three different approaches starting from the unbound partner protein structure with a range spanning a root mean square deviation of 1-2.5 Å with respect to the unbound structure. Because MC sampling is performed to select appropriate partner conformations on the fly the approach is not limited by the number of conformations in the ensemble compared to ensemble docking of each conformer pair in ensemble cross docking. Although only a fraction of generated conformers was in closer agreement with the bound structure the REMC ensemble docking approach achieved improved docking results compared to REMC docking with only the unbound partner structures or using docking energy minimization methods. The approach has significant potential for further improvement in combination with more realistic structural ensembles and better docking scoring functions. Proteins 2017; 85:924-937. © 2016 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Interference Cancellation Technique Based on Discovery of Spreading Codes of Interference Signals and Maximum Correlation Detection for DS-CDMA System

NASA Astrophysics Data System (ADS)

Hettiarachchi, Ranga; Yokoyama, Mitsuo; Uehara, Hideyuki

This paper presents a novel interference cancellation (IC) scheme for both synchronous and asynchronous direct-sequence code-division multiple-access (DS-CDMA) wireless channels. In the DS-CDMA system, the multiple access interference (MAI) and the near-far problem (NFP) are the two factors which reduce the capacity of the system. In this paper, we propose a new algorithm that is able to detect all interference signals as an individual MAI signal by maximum correlation detection. It is based on the discovery of all the unknowing spreading codes of the interference signals. Then, all possible MAI patterns so called replicas are generated as a summation of interference signals. And the true MAI pattern is found by taking correlation between the received signal and the replicas. Moreover, the receiver executes MAI cancellation in a successive manner, removing all interference signals by single-stage. Numerical results will show that the proposed IC strategy, which alleviates the detrimental effect of the MAI and the near-far problem, can significantly improve the system performance. Especially, we can obtain almost the same receiving characteristics as in the absense of interference for asynchrnous system when received powers are equal. Also, the same performances can be seen under any received power state for synchronous system.

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.

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.

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.

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.

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.

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.

Effect of simulated intraoral variables on the accuracy of a photogrammetric imaging technique for complete-arch implant prostheses.

PubMed

Bratos, Manuel; Bergin, Jumping M; Rubenstein, Jeffrey E; Sorensen, John A

2018-03-17

Conventional impression techniques to obtain a definitive cast for a complete-arch implant-supported prosthesis are technique-sensitive and time-consuming. Direct optical recording with a camera could offer an alternative to conventional impression making. The purpose of this in vitro study was to test a novel intraoral image capture protocol to obtain 3-dimensional (3D) implant spatial measurement data under simulated oral conditions of vertical opening and lip retraction. A mannequin was assembled simulating the intraoral conditions of a patient having an edentulous mandible with 5 interforaminal implants. Simulated mouth openings with 2 interincisal openings (35 mm and 55 mm) and 3 lip retractions (55 mm, 75 mm, and 85 mm) were evaluated to record the implant positions. The 3D spatial orientations of implant replicas embedded in the reference model were measured using a coordinate measuring machine (CMM) (control). Five definitive casts were made with a splinted conventional impression technique of the reference model. The positions of the implant replicas for each of the 5 casts were measured with a Nobel Procera Scanner (conventional digital method). For the prototype, optical targets were secured to the implant replicas, and 3 sets of 12 images each were recorded for the photogrammetric process of 6 groups of retractions and openings using a digital camera and a standardized image capture protocol. Dimensional data were imported into photogrammetry software (photogrammetry method). The calculated and/or measured precision and accuracy of the implant positions in 3D space for the 6 groups were compared with 1-way ANOVA with an F-test (α=.05). The precision (standard error [SE] of measurement) for CMM was 3.9 μm (95% confidence interval [CI] 2.7 to 7.1 μm). For the conventional impression method, the SE of measurement was 17.2 μm (95% CI 10.3 to 49.4 μm). For photogrammetry, a grand mean was calculated for groups MinR-AvgO, MinR-MaxO, AvgR-AvgO, and MaxR-AvgO obtaining a value of 26.8 μm (95% CI 18.1 to 51.4 μm). The overall linear measurement error for accurately locating the top center points (TCP) followed a similar pattern as for precision. CMM (coordinate measurement machine) measurement represents the nonclinical gold standard, with an average error TCP distance of 4.6 μm (95% CI 3.5 to 6 μm). All photogrammetry groups presented an accuracy that ranged from 63 μm (SD 17.6) to 47 μm (SD 9.2). The grand mean of accuracy was calculated as 55.2 μm (95% CI 8.8 to 130.8 μm). The CMM group (control) demonstrated the highest levels of accuracy and precision. Most of the groups with the photogrammetric method were statistically similar to the conventional group except for groups AvgR-MaxO and MaxR-MaxO, which represented maximum opening with average retraction and maximum opening with maximum retraction. Copyright © 2017 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Arbitrary lattice symmetries via block copolymer nanomeshes

PubMed Central

Majewski, Pawel W.; Rahman, Atikur; Black, Charles T.; Yager, Kevin G.

2015-01-01

Self-assembly of block copolymers is a powerful motif for spontaneously forming well-defined nanostructures over macroscopic areas. Yet, the inherent energy minimization criteria of self-assembly give rise to a limited library of structures; diblock copolymers naturally form spheres on a cubic lattice, hexagonally packed cylinders and alternating lamellae. Here, we demonstrate multicomponent nanomeshes with any desired lattice symmetry. We exploit photothermal annealing to rapidly order and align block copolymer phases over macroscopic areas, combined with conversion of the self-assembled organic phase into inorganic replicas. Repeated photothermal processing independently aligns successive layers, providing full control of the size, symmetry and composition of the nanoscale unit cell. We construct a variety of symmetries, most of which are not natively formed by block copolymers, including squares, rhombuses, rectangles and triangles. In fact, we demonstrate all possible two-dimensional Bravais lattices. Finally, we elucidate the influence of nanostructure on the electrical and optical properties of nanomeshes. PMID:26100566

Antireflective surface with a step in the taper: Numerical optimization and large-area fabrication

NASA Astrophysics Data System (ADS)

Shinotsuka, Kei; Hongo, Koki; Dai, Kotaro; Hirama, Satoru; Hatta, Yoshihisa

2017-02-01

In this study, we developed a practical method to improve the optical performance of subwavelength antireflective two-dimensional (2D) gratings. A numerical simulation of both convex and concave paraboloids suggested that surface reflectivity drastically decreases when a step is introduced in the taper. The optimum height and depth of a step provided average reflectances of 0.098% for convex protrusions and 0.040% for concave protrusions in the visible range. Furthermore, a stepped paraboloid was experimentally fabricated by dry etching of a Si substrate with SiO2 particle monolayer mask. A cyclo-olefin polymer (COP) reverse replica (concave) imprinted by the Si mold exhibited a measured reflectance of 0.077% on average in the visible range. It was also demonstrated that the antireflective structure was fabricated on the whole surface of a 6 in. Si wafer, which is a sufficient size for industrial utilization.

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.

Microwave vision for robots

NASA Technical Reports Server (NTRS)

Lewandowski, Leon; Struckman, Keith

1994-01-01

Microwave Vision (MV), a concept originally developed in 1985, could play a significant role in the solution to robotic vision problems. Originally our Microwave Vision concept was based on a pattern matching approach employing computer based stored replica correlation processing. Artificial Neural Network (ANN) processor technology offers an attractive alternative to the correlation processing approach, namely the ability to learn and to adapt to changing environments. This paper describes the Microwave Vision concept, some initial ANN-MV experiments, and the design of an ANN-MV system that has led to a second patent disclosure in the robotic vision field.

Developing porous ceramics on the base of zirconia oxide with thin and permeable pores by crystallization of organic additive method

NASA Astrophysics Data System (ADS)

Kamyshnaya, K. S.; Khabas, T. A.

2016-11-01

In this paper porous ceramics on the base of ZrO2 nanopowders and micropowders has been developed by freeze-casting method. A zirconia/carbamide slurry was frozen in mold and dehydrated in CaCl2 at room temperature. This simple process enabled the formation of porous ceramics with highly aligned pores as a replica of the carbamide crystals. The samples showed higher porosity of 47.9%. In addition, these materials could be used as membrane for air cleaning.

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.

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.

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

Six degree of freedom manual controls study report

NASA Technical Reports Server (NTRS)

Mckinnon, G. M.; Lippay, A.; King, M. L.

1982-01-01

The feasibility of using degree of freedom manual controls in space in an on orbit environment was determined. Several six degree of freedom controls were tested in a laboratory environment, and replica controls were used to control robot arms. The selection of six degrees of freedom as a design goal was based on the fact that six degrees are sufficient to define the location and orientation of a rigid body in space.

Historic voyage as a catalyst for inspiring change

Treesearch

Ann Melinda Bell

2007-01-01

Navigator Nainoa Thompson for Hōkūle‘a, a replica of an ancient voyaging canoe, coined the phrase, “Navigating Change,” to implant inspiration in the hearts and minds of Hawaii’s youth to take better care of their island home. Ultimately, it was about instilling hope and a cultural based value of responsibility in our younger generation. In 2001, the...

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.

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

Toward large-area roll-to-roll printed nanophotonic sensors

NASA Astrophysics Data System (ADS)

Karioja, Pentti; Hiltunen, Jussi; Aikio, Sanna M.; Alajoki, Teemu; Tuominen, Jarkko; Hiltunen, Marianne; Siitonen, Samuli; Kontturi, Ville; Böhlen, Karl; Hauser, Rene; Charlton, Martin; Boersma, Arjen; Lieberzeit, Peter; Felder, Thorsten; Eustace, David; Haskal, Eliav

2014-05-01

Polymers have become an important material group in fabricating discrete photonic components and integrated optical devices. This is due to their good properties: high optical transmittance, versatile processability at relative low temperatures and potential for low-cost production. Recently, nanoimprinting or nanoimprint lithography (NIL) has obtained a plenty of research interest. In NIL, a mould is pressed against a substrate coated with a moldable material. After deformation of the material, the mold is separated and a replica of the mold is formed. Compared with conventional lithographic methods, imprinting is simple to carry out, requires less-complicated equipment and can provide high-resolution with high throughput. Nanoimprint lithography has shown potential to become a method for low-cost and high-throughput fabrication of nanostructures. We show the development process of nano-structured, large-area multi-parameter sensors using Photonic Crystal (PC) and Surface Enhanced Raman Scattering (SERS) methodologies for environmental and pharmaceutical applications. We address these challenges by developing roll-to-roll (R2R) UV-nanoimprint fabrication methods. Our development steps are the following: Firstly, the proof of concept structures are fabricated by the use of wafer-level processes in Si-based materials. Secondly, the master molds of successful designs are fabricated, and they are used to transfer the nanophotonic structures into polymer materials using sheet-level UV-nanoimprinting. Thirdly, the sheet-level nanoimprinting processes are transferred to roll-to-roll fabrication. In order to enhance roll-to-roll manufacturing capabilities, silicone-based polymer material development was carried out. In the different development phases, Photonic Crystal and SERS sensor structures with increasing complexities were fabricated using polymer materials in order to enhance sheet-level and roll-to-roll manufacturing processes. In addition, chemical and molecular imprint (MIP) functionalization methods were applied in the sensor demonstrators. In this paper, the process flow in fabricating large-area nanophotonic structures by the use of sheet-level and roll-to-roll UV- nanoimprinting is reported.

Determining spherical lens correction for astronaut training underwater.

PubMed

Porter, Jason; Gibson, C Robert; Strauss, Samuel

2011-09-01

To develop a model that will accurately predict the distance spherical lens correction needed to be worn by National Aeronautics and Space Administration astronauts while training underwater. The replica space suit's helmet contains curved visors that induce refractive power when submersed in water. Anterior surface powers and thicknesses were measured for the helmet's protective and inside visors. The impact of each visor on the helmet's refractive power in water was analyzed using thick lens calculations and Zemax optical design software. Using geometrical optics approximations, a model was developed to determine the optimal distance spherical power needed to be worn underwater based on the helmet's total induced spherical power underwater and the astronaut's manifest spectacle plane correction in air. The validity of the model was tested using data from both eyes of 10 astronauts who trained underwater. The helmet's visors induced a total power of -2.737 D when placed underwater. The required underwater spherical correction (FW) was linearly related to the spectacle plane spherical correction in air (FAir): FW = FAir + 2.356 D. The mean magnitude of the difference between the actual correction worn underwater and the calculated underwater correction was 0.20 ± 0.11 D. The actual and calculated values were highly correlated (r = 0.971) with 70% of eyes having a difference in magnitude of <0.25 D between values. We devised a model to calculate the spherical spectacle lens correction needed to be worn underwater by National Aeronautics and Space Administration astronauts. The model accurately predicts the actual values worn underwater and can be applied (more generally) to determine a suitable spectacle lens correction to be worn behind other types of masks when submerged underwater.

Determining spherical lens correction for astronaut training underwater

PubMed Central

Porter, Jason; Gibson, C. Robert; Strauss, Samuel

2013-01-01

Purpose To develop a model that will accurately predict the distance spherical lens correction needed to be worn by National Aeronautics and Space Administration (NASA) astronauts while training underwater. The replica space suit’s helmet contains curved visors that induce refractive power when submersed in water. Methods Anterior surface powers and thicknesses were measured for the helmet’s protective and inside visors. The impact of each visor on the helmet’s refractive power in water was analyzed using thick lens calculations and Zemax optical design software. Using geometrical optics approximations, a model was developed to determine the optimal distance spherical power needed to be worn underwater based on the helmet’s total induced spherical power underwater and the astronaut’s manifest spectacle plane correction in air. The validity of the model was tested using data from both eyes of 10 astronauts who trained underwater. Results The helmet visors induced a total power of −2.737 D when placed underwater. The required underwater spherical correction (FW) was linearly related to the spectacle plane spherical correction in air (FAir): FW = FAir + 2.356 D. The mean magnitude of the difference between the actual correction worn underwater and the calculated underwater correction was 0.20 ± 0.11 D. The actual and calculated values were highly correlated (R = 0.971) with 70% of eyes having a difference in magnitude of < 0.25 D between values. Conclusions We devised a model to calculate the spherical spectacle lens correction needed to be worn underwater by National Aeronautics and Space Administration astronauts. The model accurately predicts the actual values worn underwater and can be applied (more generally) to determine a suitable spectacle lens correction to be worn behind other types of masks when submerged underwater. PMID:21623249

High-throughput state-machine replication using software transactional memory.

PubMed

Zhao, Wenbing; Yang, William; Zhang, Honglei; Yang, Jack; Luo, Xiong; Zhu, Yueqin; Yang, Mary; Luo, Chaomin

2016-11-01

State-machine replication is a common way of constructing general purpose fault tolerance systems. To ensure replica consistency, requests must be executed sequentially according to some total order at all non-faulty replicas. Unfortunately, this could severely limit the system throughput. This issue has been partially addressed by identifying non-conflicting requests based on application semantics and executing these requests concurrently. However, identifying and tracking non-conflicting requests require intimate knowledge of application design and implementation, and a custom fault tolerance solution developed for one application cannot be easily adopted by other applications. Software transactional memory offers a new way of constructing concurrent programs. In this article, we present the mechanisms needed to retrofit existing concurrency control algorithms designed for software transactional memory for state-machine replication. The main benefit for using software transactional memory in state-machine replication is that general purpose concurrency control mechanisms can be designed without deep knowledge of application semantics. As such, new fault tolerance systems based on state-machine replications with excellent throughput can be easily designed and maintained. In this article, we introduce three different concurrency control mechanisms for state-machine replication using software transactional memory, namely, ordered strong strict two-phase locking, conventional timestamp-based multiversion concurrency control, and speculative timestamp-based multiversion concurrency control. Our experiments show that speculative timestamp-based multiversion concurrency control mechanism has the best performance in all types of workload, the conventional timestamp-based multiversion concurrency control offers the worst performance due to high abort rate in the presence of even moderate contention between transactions. The ordered strong strict two-phase locking mechanism offers the simplest solution with excellent performance in low contention workload, and fairly good performance in high contention workload.

High-throughput state-machine replication using software transactional memory

PubMed Central

Yang, William; Zhang, Honglei; Yang, Jack; Luo, Xiong; Zhu, Yueqin; Yang, Mary; Luo, Chaomin

2017-01-01

State-machine replication is a common way of constructing general purpose fault tolerance systems. To ensure replica consistency, requests must be executed sequentially according to some total order at all non-faulty replicas. Unfortunately, this could severely limit the system throughput. This issue has been partially addressed by identifying non-conflicting requests based on application semantics and executing these requests concurrently. However, identifying and tracking non-conflicting requests require intimate knowledge of application design and implementation, and a custom fault tolerance solution developed for one application cannot be easily adopted by other applications. Software transactional memory offers a new way of constructing concurrent programs. In this article, we present the mechanisms needed to retrofit existing concurrency control algorithms designed for software transactional memory for state-machine replication. The main benefit for using software transactional memory in state-machine replication is that general purpose concurrency control mechanisms can be designed without deep knowledge of application semantics. As such, new fault tolerance systems based on state-machine replications with excellent throughput can be easily designed and maintained. In this article, we introduce three different concurrency control mechanisms for state-machine replication using software transactional memory, namely, ordered strong strict two-phase locking, conventional timestamp-based multiversion concurrency control, and speculative timestamp-based multiversion concurrency control. Our experiments show that speculative timestamp-based multiversion concurrency control mechanism has the best performance in all types of workload, the conventional timestamp-based multiversion concurrency control offers the worst performance due to high abort rate in the presence of even moderate contention between transactions. The ordered strong strict two-phase locking mechanism offers the simplest solution with excellent performance in low contention workload, and fairly good performance in high contention workload. PMID:29075049

Superficial Macromolecular Arrays on the Cell Wall of Spirillum putridiconchylium

PubMed Central

Beveridge, T. J.; Murray, R. G. E.

1974-01-01

Electron microscopy of the cell envelope of Spirillum putridiconchylium, using negatively stained, thin-sectioned, and replicated freeze-etched preparations, showed two superficial wall layers forming a complex macromolecular pattern on the external surface. The outer structured layer was a linear array of particles overlying an inner tetragonal array of larger subunits. They were associated in a very regular fashion, and the complex was bonded to the outer, pitted surface of the lipopolysaccharide tripartite layer of the cell wall. The relationship of the components of the two structured layers was resolved with the aid of optical diffraction, combined with image filtering and reconstruction and linear and rotary integration techniques. The outer structural layer consisted of spherical 1.5-nm units set in double lines determined by the size and arrangement of 6- by 3-nm inner structural layer subunits, which bore one outer structural layer unit on each outer corner. The total effect of this arrangement was a double-ridged linear structure that was evident in surface replicas and negatively stained fragments of the whole wall. The packing of these units was not square but skewed by 2° off the perpendicular so that the “unit array” described by optical diffraction and linear integration appeared to be a deformed tetragon. The verity of the model was checked by using a photographically reduced image to produce an optical diffraction pattern for comparison with that of the actual layers. The correspondence was nearly perfect. Images PMID:4137219

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.

LOAPEX: The Long-Range Ocean Acoustic Propagation EXperiment

DTIC Science & Technology

2009-01-01

roughly 4200 m, the OBS/H packages at 5000 m received the LOAPEX transmissions. 4) Signal Processing : In general, signal processing for all receptions is...coherently in the time domain. To optimize processing , is based on the coherence time of the received signal and the resulting pro- cessing gain is . The...replica of the transmission. This process produces a triangular-shaped pulse with a time resolution of 1-b length, or 27 ms, and additional processing

Self-assembly and bilayer-micelle transition of fatty acids studied by replica-exchange constant pH molecular dynamics

PubMed Central

Morrow, Brian H.; Koenig, Peter H.; Shen, Jana K.

2014-01-01

Recent interest in the development of surfactant-based nano delivery systems targeting tumor sites has sparked our curiosity to understand the detailed mechanism of the self-assembly and phase transitions of pH-sensitive surfactants. Towards this goal we applied a state-of-the-art simulation technique, continuous constant pH molecular dynamics (CpHMD) with the hybrid-solvent scheme and pH-based replica-exchange protocol, to study de novo self-assembly of 30 and 40 lauric acids, a simple model titratable surfactant. We observed the formation of a gel-state bilayer at low and intermediate pH and a spherical micelle at high pH, with the phase transition starting at 20–30% ionization and completing at 50%. The degree of cooperativity for the transition increases from the 30-mer to the 40-mer. The calculated apparent or bulk pKa value is 7.0 for the 30-mer and 7.5 for the 40-mer. Congruent with experiment, these data demonstrate that CpHMD is capable of accurately modeling large conformational transitions of surfactant systems while allowing simultaneous proton titration of constituent molecules. We suggest that CpHMD simulations may become a useful tool to aid in the design and development of pH-sensitive nanocarriers for a variety of biomedical and technological applications. PMID:24215478

Applications of stereolithography for rapid prototyping of biologically compatible chip-based physiometers

NASA Astrophysics Data System (ADS)

Fuad, Nurul Mohd; Zhu, Feng; Kaslin, Jan; Wlodkowic, Donald

2016-12-01

Despite the growing demand and numerous applications for the biomedical community, the developments in millifluidic devices for small model organisms are limited compared to other fields of biomicrofluidics. The main reasons for this stagnanation are difficulties in prototyping of millimeter scale and high aspect ratio devices needed for large metazoan organisms. Standard photolithography is in this context a time consuming procedure not easily adapted for fabrication of molds with vertical dimensions above 1 mm. Moreover, photolithography is still largely unattainable to a gross majority of biomedical laboratories willing to pursue custom development of their own chip-based platforms due to costs and need for dedicated clean room facilities. In this work, we present application of high-definition additive manufacturing systems for fabrication of 3D printed moulds used in soft lithography. Combination of 3D printing with PDMS replica molding appears to be an alternative for millifluidic systems that yields rapid and cost effective prototyping pipeline. We investigated the important aspects on both 3D printed moulds and PDMS replicas such as geometric accuracies and surface topology. Our results demonstrated that SLA technologies could be applied for rapid and accurate fabrication of millifluidic devices for trapping of millimetre-sized specimens such as living zebrafish larvae. We applied the new manufacturing method in a proof-of-concept prototype device capable of trapping and immobilizing living zebrafish larvae for recording heart rate variation in cardio-toxicity experiments.

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.

Cloning SU8 silicon masters using epoxy resins to increase feature replicability and production for cell culture devices.

PubMed

Kamande, J W; Wang, Y; Taylor, A M

2015-05-01

In recent years, there has been a dramatic increase in the use of poly(dimethylsiloxane) (PDMS) devices for cell-based studies. Commonly, the negative tone photoresist, SU8, is used to pattern features onto silicon wafers to create masters (SU8-Si) for PDMS replica molding. However, the complexity in the fabrication process, low feature reproducibility (master-to-master variability), silane toxicity, and short life span of these masters have been deterrents for using SU8-Si masters for the production of cell culture based PDMS microfluidic devices. While other techniques have demonstrated the ability to generate multiple devices from a single master, they often do not match the high feature resolution (∼0.1 μm) and low surface roughness that soft lithography masters offer. In this work, we developed a method to fabricate epoxy-based masters that allows for the replication of features with high fidelity directly from SU8-Si masters via their PDMS replicas. By this method, we show that we could obtain many epoxy based masters with equivalent features to a single SU8-Si master with a low feature variance of 1.54%. Favorable feature transfer resolutions were also obtained by using an appropriate Tg epoxy based system to ensure minimal shrinkage of features ranging in size from ∼100 μm to <10 μm in height. We further show that surface coating epoxy masters with Cr/Au lead to effective demolding and yield PDMS chambers that are suitable for long-term culturing of sensitive primary hippocampal neurons. Finally, we incorporated pillars within the Au-epoxy masters to eliminate the process of punching media reservoirs and thereby reducing substantial artefacts and wastage.

Cloning SU8 silicon masters using epoxy resins to increase feature replicability and production for cell culture devices

PubMed Central

Kamande, J. W.; Wang, Y.; Taylor, A. M.

2015-01-01

In recent years, there has been a dramatic increase in the use of poly(dimethylsiloxane) (PDMS) devices for cell-based studies. Commonly, the negative tone photoresist, SU8, is used to pattern features onto silicon wafers to create masters (SU8-Si) for PDMS replica molding. However, the complexity in the fabrication process, low feature reproducibility (master-to-master variability), silane toxicity, and short life span of these masters have been deterrents for using SU8-Si masters for the production of cell culture based PDMS microfluidic devices. While other techniques have demonstrated the ability to generate multiple devices from a single master, they often do not match the high feature resolution (∼0.1 μm) and low surface roughness that soft lithography masters offer. In this work, we developed a method to fabricate epoxy-based masters that allows for the replication of features with high fidelity directly from SU8-Si masters via their PDMS replicas. By this method, we show that we could obtain many epoxy based masters with equivalent features to a single SU8-Si master with a low feature variance of 1.54%. Favorable feature transfer resolutions were also obtained by using an appropriate Tg epoxy based system to ensure minimal shrinkage of features ranging in size from ∼100 μm to <10 μm in height. We further show that surface coating epoxy masters with Cr/Au lead to effective demolding and yield PDMS chambers that are suitable for long-term culturing of sensitive primary hippocampal neurons. Finally, we incorporated pillars within the Au-epoxy masters to eliminate the process of punching media reservoirs and thereby reducing substantial artefacts and wastage. PMID:26180572

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.

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.

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

Equilibrium Molecular Thermodynamics from Kirkwood Sampling

PubMed Central

2015-01-01

We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys.2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide. PMID:25915525

Supersoft lithography: Candy-based fabrication of soft silicone microstructures

PubMed Central

Moraes, Christopher; Labuz, Joseph M.; Shao, Yue; Fu, Jianping; Takayama, Shuichi

2015-01-01

We designed a fabrication technique able to replicate microstructures in soft silicone materials (E < 1 kPa). Sugar-based ‘hard candy’ recipes from the confectionery industry were modified to be compatible with silicone processing conditions, and used as templates for replica molding. Microstructures fabricated in soft silicones can then be easily released by dissolving the template in water. We anticipate that this technique will be of particular importance in replicating physiologically soft, microstructured environments for cell culture, and demonstrate a first application in which intrinsically soft microstructures are used to measure forces generated by fibroblast-laden contractile tissues. PMID:26245893

Supersoft lithography: candy-based fabrication of soft silicone microstructures.

PubMed

Moraes, Christopher; Labuz, Joseph M; Shao, Yue; Fu, Jianping; Takayama, Shuichi

2015-01-01

We designed a fabrication technique able to replicate microstructures in soft silicone materials (E < 1 kPa). Sugar-based 'hard candy' recipes from the confectionery industry were modified to be compatible with silicone processing conditions, and used as templates for replica molding. Microstructures fabricated in soft silicones can then be easily released by dissolving the template in water. We anticipate that this technique will be of particular importance in replicating physiologically soft, microstructured environments for cell culture, and demonstrate a first application in which intrinsically soft microstructures are used to measure forces generated by fibroblast-laden contractile tissues.

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

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.

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.

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.

Liquid-glass transition in equilibrium

NASA Astrophysics Data System (ADS)

Parisi, G.; Seoane, B.

2014-02-01

We show in numerical simulations that a system of two coupled replicas of a binary mixture of hard spheres undergoes a phase transition in equilibrium at a density slightly smaller than the glass transition density for an unreplicated system. This result is in agreement with the theories that predict that such a transition is a precursor of the standard ideal glass transition. The critical properties are compatible with those of an Ising system. The relations of this approach to the conventional approach based on configurational entropy are briefly discussed.

Evaluation of Rock Joint Coefficients

NASA Astrophysics Data System (ADS)

Audy, Ondřej; Ficker, Tomáš

2017-10-01

A computer method for evaluation of rock joint coefficients is described and several applications are presented. The method is based on two absolute numerical indicators that are formed by means of the Fourier replicas of rock joint profiles. The first indicator quantifies the vertical depth of profiles and the second indicator classifies wavy character of profiles. The absolute indicators have replaced the formerly used relative indicators that showed some artificial behavior in some cases. This contribution is focused on practical computations testing the functionality of the newly introduced indicators.

Calculation of Protein Heat Capacity from Replica-Exchange Molecular Dynamics Simulations with Different Implicit Solvent Models

DTIC Science & Technology

2008-10-30

rigorous Poisson-based methods generally apply a Lee-Richards mo- lecular surface.9 This surface is considered the de facto description for continuum...definition and calculation of the Born radii. To evaluate the Born radii, two approximations are invoked. The first is the Coulomb field approximation (CFA...energy term, and depending on the particular GB formulation, higher-order non- Coulomb correction terms may be added to the Born radii to account for the

An Economic Case for End System Multicast

NASA Astrophysics Data System (ADS)

Analoui, Morteza; Rezvani, Mohammad Hossein

This paper presents a non-strategic model for the end-system multicast networks based on the concept of replica exchange economy. We believe that microeconomics is a good candidate to investigate the problem of selfishness of the end-users (peers) in order to maximize the aggregate throughput. In this solution concept, the decisions that a peer might make, does not affect the actions of the other peers at all. The proposed mechanism tunes the price of the service in such a way that general equilibrium holds.

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.

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.

Wafer-level manufacturing technology of glass microlenses

NASA Astrophysics Data System (ADS)

Gossner, U.; Hoeftmann, T.; Wieland, R.; Hansch, W.

2014-08-01

In high-tech products, there is an increasing demand to integrate glass lenses into complex micro systems. Especially in the lighting industry LEDs and laser diodes used for automotive applications require encapsulated micro lenses. To enable low-cost production, manufacturing of micro lenses on wafer level base using a replication technology is a key technology. This requires accurate forming of thousands of lenses with a diameter of 1-2 mm on a 200 mm wafer compliant with mass production. The article will discuss the technical aspects of a lens manufacturing replication process and the challenges, which need to be solved: choice of an appropriate master for replication, thermally robust interlayer coating, choice of replica glass, bonding and separation procedure. A promising approach for the master substrate material is based on a lens structured high-quality glass wafer with high melting point covered by a coating layer of amorphous silicon or germanium. This layer serves as an interlayer for the glass bonding process. Low pressure chemical vapor deposition and plasma enhanced chemical vapor deposition processes allow a deposition of layer coatings with different hydrogen and doping content influencing their chemical and physical behavior. A time reduced molding process using a float glass enables the formation of high quality lenses while preserving the recyclability of the mother substrate. The challenge is the separation of the replica from the master mold. An overview of chemical methods based on optimized etching of coating layer through small channels will be given and the impact of glass etching on surface roughness is discussed.

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

PubMed Central

2015-01-01

We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values. PMID:25061443

Duplex-imprinted nano well arrays for promising nanoparticle assembly

NASA Astrophysics Data System (ADS)

Li, Xiangping; Manz, Andreas

2018-02-01

A large area nano-duplex-imprint technique is presented in this contribution using natural cicada wings as stamps. The glassy wings of the cicada, which are abundant in nature, exhibit strikingly interesting nanopillar structures over their membrane. This technique, with excellent performance despite the nonplanar surface of the wings, combines both top-down and bottom-up nanofabrication techniques. It transitions micro-nanofabrication from a cleanroom environment to the bench. Two different materials, dicing tape with an acrylic layer and a UV optical adhesive, are used to make replications at the same time, thus achieving duplex imprinting. The promise of a large volume of commercial manufacturing of these nanostructure elements can be envisaged through this contribution to speeding up the fabrication process and achieving a higher throughput. The contact angle of the replicated nanowell arrays before and after oxygen plasma was measured. Gold nanoparticles (50 nm) were used to test how the nanoparticles behaved on the untreated and plasma-treated replica surface. The experiments show that promising nanoparticle self-assembly can be obtained.

Investigation of room temperature UV emission of ZnO films with different defect densities induced by laser irradiation.

PubMed

Zhao, Yan; Jiang, Yijian

2010-08-01

We studied the room temperature UV emission of ZnO films with different defect densities which is fabricated by KrF laser irradiation process. It is shown room temperature UV photoluminescence of ZnO film is composed of contribution from free-exciton (FX) recombination and its longitudinal-optical phonon replica (FX-LO) (1LO, 2LO). With increase of the defect density, the FX emission decreased and FX-LO emission increased dramatically; and the relative strengths of FX to FX-LO emission intensities determine the peak position and intensity of UV emission. What is more, laser irradiation with moderate energy density could induce the crystalline ZnO film with very flat and smooth surface. This investigation indicates that KrF laser irradiation could effectively modulate the exciton emission and surface morphology, which is important for the application of high performance of UV emitting optoelectronic devices. Copyright 2010 Elsevier B.V. All rights reserved.

Noiseless intensity amplification of repetitive signals by coherent addition using the temporal Talbot effect

PubMed Central

Maram, Reza; Van Howe, James; Li, Ming; Azaña, José

2014-01-01

Amplification of signal intensity is essential for initiating physical processes, diagnostics, sensing, communications and measurement. During traditional amplification, the signal is amplified by multiplying the signal carriers through an active gain process, requiring the use of an external power source. In addition, the signal is degraded by noise and distortions that typically accompany active gain processes. We show noiseless intensity amplification of repetitive optical pulse waveforms with gain from 2 to ~20 without using active gain. The proposed method uses a dispersion-induced temporal self-imaging (Talbot) effect to redistribute and coherently accumulate energy of the original repetitive waveforms into fewer replica waveforms. In addition, we show how our passive amplifier performs a real-time average of the wave-train to reduce its original noise fluctuation, as well as enhances the extinction ratio of pulses to stand above the noise floor. Our technique is applicable to repetitive waveforms in any spectral region or wave system. PMID:25319207

Saw-tooth refractive x-ray optics with sub-micron resolution

NASA Astrophysics Data System (ADS)

Cederstrom, Bjorn; Ribbing, Carolina; Lundqvist, Mats

2002-11-01

Saw-tooth refractive x-ray lenses have been used to focus a synchrotron beam to sub-μm line width. These lenses are free from spherical aberration and work in analogy with 1-D focusing parabolic compound refractive lenses. However, the focal length can be varied by a simple mechanical procedure. Silicon lenses were fabricated by wet anisotropic etching, and epoxy replicas were molded from the silicon masters. Theses lenses provided 1-D intensity gains up to a factor of 40 and the smallest focal line width was 0.74 μm, very close to the theoretical expectation. Two crossed lenses were put in series to obtain 2-D focusing and the 80 μm by 275 μm source was imaged to 1.0 μm by 5.4 μm. Beryllium lenses were fabricated using conventional computer-controlled milling. The focal line width was 1.7 μm, nearly 3 times larger than predicted by theory. This can be attributed to large surface roughness and a bent lens shape.

Large-k exciton dynamics in GaN epilayers: Nonthermal and thermal regimes

NASA Astrophysics Data System (ADS)

Vinattieri, Anna; Bogani, Franco; Cavigli, Lucia; Manzi, Donatella; Gurioli, Massimo; Feltin, Eric; Carlin, Jean-François; Martin, Denis; Butté, Raphaël; Grandjean, Nicolas

2013-02-01

We present a detailed investigation performed at low temperature (T<50 K) concerning the exciton dynamics in GaN epilayers grown on c-plane sapphire substrates, focusing on the exciton formation and the transition from the nonthermal to the thermal regime. The time-resolved kinetics of longitudinal-optical-phonon replicas is used to address the energy relaxation in the excitonic band. From picosecond time-resolved spectra, we bring evidence for a long lasting nonthermal excitonic distribution, which accounts for the first 50 ps. Such a behavior is confirmed in different experimental conditions when both nonresonant and resonant excitations are used. At low excitation power density, the exciton formation and their subsequent thermalization are dominated by impurity scattering rather than by acoustic phonon scattering. The estimate of the average energy of the excitons as a function of delay after the excitation pulse provides information on the relaxation time, which describes the evolution of the exciton population to the thermal regime.

On the identification of folium and orchil on illuminated manuscripts

NASA Astrophysics Data System (ADS)

Aceto, Maurizio; Calà, Elisa; Agostino, Angelo; Fenoglio, Gaia; Idone, Ambra; Porter, Cheryl; Gulmini, Monica

2017-01-01

The identification of the two purple dyes folium and orchil has rarely been reported in the analysis of painted artworks, especially when analysing illuminated manuscripts. This is not consistent with the fact that ancient literary sources suggested their use as substitutes for the more expensive Tyrian purple dye. By employing non-invasive spectroscopic techniques, the present work demonstrates that these dyes were actually widely used in the production of ancient manuscripts. By employing UV-visible diffuse reflectance spectrophotometry with optic fibres (FORS) and spectrofluorimetry, the abundant identification of both dyes on medieval manuscripts was performed by comparing the spectra recorded on ancient codices with those obtained on accurate replicas of dyed or painted parchment. Moreover, examples are also reported whereby the considered purple dyes were used in mixtures with other colourants. The overall information obtained here allowed us to define new boundaries for the time range in which orchil and folium dyes were used which is wider than previously thought, and to focus on their particular uses in the decoration of books.

Broadband two-dimensional electronic spectroscopy in an actively phase stabilized pump-probe configuration.

PubMed

Zhu, Weida; Wang, Rui; Zhang, Chunfeng; Wang, Guodong; Liu, Yunlong; Zhao, Wei; Dai, Xingcan; Wang, Xiaoyong; Cerullo, Giulio; Cundiff, Steven; Xiao, Min

2017-09-04

We introduce a novel configuration for two-dimensional electronic spectroscopy (2DES) that combines the partially collinear pump-probe geometry with active phase locking. We demonstrate the method on a solution sample of CdSe/ZnS nanocrystals by employing two non-collinear optical parametric amplifiers as the pump and probe sources. The two collinear pump pulse replicas are created using a Mach-Zehnder interferometer phase stabilized by active feedback electronics. Taking the advantage of separated paths of the two pump pulses in the interferometer, we improve the signal-to-noise ratio with double modulation of the individual pump beams. In addition, a quartz wedge pair manipulates the phase difference between the two pump pulses, enabling the recovery of the rephasing and non-rephasing signals. Our setup integrates many advantages of available 2DES techniques with robust phase stabilization, ultrafast time resolution, two-color operation, long delay scan, individual polarization manipulation and the ease of implementation.

Multi-resonant plasmonic nanodome arrays for label-free biosensing applications

NASA Astrophysics Data System (ADS)

Choi, Charles J.; Semancik, Steve

2013-08-01

The characteristics and utility of plasmonic nanodome arrays capable of supporting multiple resonance modes are described. A low-cost, large-area replica molding process is used to produce, on flexible plastic substrates, two-dimensional periodic arrays of cylinders that are subsequently coated with SiO2 and Ag thin films to form dome-shaped structures, with 14 nm spacing between the features, in a precise and reproducible fashion. Three distinct optical resonance modes, a grating diffraction mode and two localized surface plasmon resonance (LSPR) modes, are observed experimentally and confirmed by finite-difference-time-domain (FDTD) modeling which is used to calculate the electromagnetic field distribution of each resonance around the nanodome array structure. Each optical mode is characterized by measuring sensitivity to bulk refractive index changes and to surface effects, which are examined using stacked polyelectrolyte layers. The utility of the plasmonic nanodome array as a functional interface for biosensing applications is demonstrated by performing a bioassay to measure the binding affinity constant between protein A and human immunoglobulin G (IgG) as a model system. The nanoreplica molding process presented in this work allows for simple, inexpensive, high-throughput fabrication of nanoscale plasmonic structures over a large surface area (120 × 120 mm2) without the requirement for high resolution lithography or additional processes such as etching or liftoff. The availability of multiple resonant modes, each with different optical properties, allows the nanodome array surface to address a wide range of biosensing problems with various target analytes of different sizes and configurations.

Response of human corneal fibroblasts on silk film surface patterns.

PubMed

Gil, Eun Seok; Park, Sang-Hyug; Marchant, Jeff; Omenetto, Fiorenzo; Kaplan, David L

2010-06-11

Transparent, biodegradable, mechanically robust, and surface-patterned silk films were evaluated for the effect of surface morphology on human corneal fibroblast (hCF) cell proliferation, orientation, and ECM deposition and alignment. A series of dimensionally different surface groove patterns were prepared from optically graded glass substrates followed by casting poly(dimethylsiloxane) (PDMS) replica molds. The features on the patterned silk films showed an array of asymmetric triangles and displayed 37-342 nm depths and 445-3 582 nm widths. hCF DNA content on all patterned films were not significantly different from that on flat silk films after 4 d in culture. However, the depth and width of the grooves influenced cell alignment, while the depth differences affected cell orientation; overall, deeper and narrower grooves induced more hCF orientation. Over 14 d in culture, cell layers and actin filament organization demonstrated that confluent hCFs and their cytoskeletal filaments were oriented along the direction of the silk film patterned groove axis. Collagen type V and proteoglycans (decorin and biglycan), important markers of corneal stromal tissue, were highly expressed with alignment. Understanding corneal stromal fibroblast responses to surface features on a protein-based biomaterial applicable in vivo for corneal repair potential suggests options to improve corneal tissue mimics. Further, the approaches provide fundamental biomaterial designs useful for bioengineering oriented tissue layers, an endemic feature in most biological tissue structures that lead to critical tissue functions.

Nanostructured Surfaces and Detection Instrumentation for Photonic Crystal Enhanced Fluorescence

PubMed Central

Chaudhery, Vikram; George, Sherine; Lu, Meng; Pokhriyal, Anusha; Cunningham, Brian T.

2013-01-01

Photonic crystal (PC) surfaces have been demonstrated as a compelling platform for improving the sensitivity of surface-based fluorescent assays used in disease diagnostics and life science research. PCs can be engineered to support optical resonances at specific wavelengths at which strong electromagnetic fields are utilized to enhance the intensity of surface-bound fluorophore excitation. Meanwhile, the leaky resonant modes of PCs can be used to direct emitted photons within a narrow range of angles for more efficient collection by a fluorescence detection system. The multiplicative effects of enhanced excitation combined with enhanced photon extraction combine to provide improved signal-to-noise ratios for detection of fluorescent emitters, which in turn can be used to reduce the limits of detection of low concentration analytes, such as disease biomarker proteins. Fabrication of PCs using inexpensive manufacturing methods and materials that include replica molding on plastic, nano-imprint lithography on quartz substrates result in devices that are practical for single-use disposable applications. In this review, we will describe the motivation for implementing high-sensitivity fluorescence detection in the context of molecular diagnosis and gene expression analysis though the use of PC surfaces. Recent efforts to improve the design and fabrication of PCs and their associated detection instrumentation are summarized, including the use of PCs coupled with Fabry-Perot cavities and external cavity lasers. PMID:23624689

Molding mineral within microporous hydrogels by a polymer-induced liquid-precursor (PILP) process.

PubMed

Cheng, Xingguo; Gower, Laurie B

2006-01-01

Natural biominerals often have exquisite morphologies, where the cells exercise a high degree of crystallographic control through secretion of biological macromolecules and regulation of ion transport. One important example is the sea urchin spine. It has recently been shown to be formed through deposition of a transient amorphous calcium carbonate (ACC) precursor phase that later transforms to single-crystalline calcite, ultimately forming an elaborate three-dimensional microporous calcium carbonate structure with interconnected pores. Macromolecules associated with the mineral phase are thought to play a key role in regulating this transformation. The work described here mimics this type of morphological control by "molding" an amorphous calcium carbonate precursor within a porous poly(2-hydroxyethyl methacrylate) (PHEMA) hydrogel that has been prepared as a negative replica from the void space of an urchin spine. Using an acidic biomimetic polymer as a process-directing agent, we show that polyaspartic acid induces amorphous calcium carbonate (ACC) nanoparticles, which have fluidic character and therefore are able to infiltrate the PHEMA hydrogel replica and coalesce into the convoluted morphology that replicates the original microporous structure of the sea urchin spine. By "molding" calcium carbonate into a complex morphology at room temperature, using a precursor process that is induced by a biomimetic acidic macromolecule, the PILP process is a useful in vitro model for examining different aspects of the amorphous-to-crystalline transformation process that is apparently used by a variety of biomineralizing organisms. For example, although we were able to replicate the overall morphology of the spine, it had polycrystalline texture; further studies with this system will focus on controlling the nucleation event, which may help to elucidate how such a convoluted structure can be prepared with single-crystalline texture via an amorphous precursor. Through a better understanding of the mechanisms used by organisms to regulate crystal properties, such biomimetic processes can lead to the synthesis of materials with superior electronic, mechanical, and optical properties.

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.

High index glass thin film processing for photonics and photovoltaic (PV) applications

NASA Astrophysics Data System (ADS)

Ogbuu, Okechukwu Anthony

To favorably compete with fossil-fuel technology, the greatest challenge for thin film solar-cells is to improve efficiency and reduce material cost. Thickness scaling to thin film reduces material cost but affects the light absorption in the cells; therefore a concept that traps incident photons and increases its optical path length is needed to boost absorption in thin film solar cells. One approach is the integration of low symmetric gratings (LSG), using high index material, on either the front-side or backside of 30 um thin c-Si cells. In this study, Multicomponent TeO2--Bi2O 3--ZnO (TBZ) glass thin films were prepared using RF magnetron sputtering under different oxygen flow rates. The influences of oxygen flow rate on the structural and optical properties of the resulting thin films were investigated. The structural origin of the optical property variation was studied using X-ray diffraction, X-ray photoelectron spectroscopy, Raman Spectroscopy, and transmission electron microscopy. The results indicate that TBZ glass thin film is a suitable material for front side LSG material photovoltaic and photonics applications due to their amorphous nature, high refractive index (n > 2), broad band optical transparency window, low processing temperature. We developed a simple maskless method to pattern sputtered tellurite based glass thin films using unconventional agarose hydrogel mediated wet etching. Conventional wet etching process, while claiming low cost and high throughput, suffers from reproducibility and pattern fidelity issues due to the isotropic nature of wet chemical etching when applied to glasses and polymers. This method overcomes these challenges by using an agarose hydrogel stamp to mediate a conformal etching process. In our maskless method, agarose hydrogel stamps are patterned following a standard soft lithography and replica molding process from micropatterned masters and soaked in a chemical etchant. The micro-scale features on the stamp are subsequently transferred into glass and polymer thin films via conformal wet etching. High refractive index chalcogenide glass (n = 2.6) thin films with composition As20Se80 was selected for backside LSG material due to their attractive properties. We developed an optimized integration protocol for LSG integration and successfully integrated these LSG structures at the back side of both 30 microm c-Si solar cells and standalone 30 microm c-Si wafers. Optical and electrical characterization of LSG on thin c-Si cells shows that LSG structures create higher absorption enhancement and external quantum efficiency at long wavelengths.

Exploring the binding pathways of the 14-3-3ζ protein: Structural and free-energy profiles revealed by Hamiltonian replica exchange molecular dynamics with distancefield distance restraints

PubMed Central

Nagy, Gabor; Oostenbrink, Chris; Hritz, Jozef

2017-01-01

The 14-3-3 protein family performs regulatory functions in eukaryotic organisms by binding to a large number of phosphorylated protein partners. Whilst the binding mode of the phosphopeptides within the primary 14-3-3 binding site is well established based on the crystal structures of their complexes, little is known about the binding process itself. We present a computational study of the process by which phosphopeptides bind to the 14-3-3ζ protein. Applying a novel scheme combining Hamiltonian replica exchange molecular dynamics and distancefield restraints allowed us to map and compare the most likely phosphopeptide-binding pathways to the 14-3-3ζ protein. The most important structural changes to the protein and peptides involved in the binding process were identified. In order to bind phosphopeptides to the primary interaction site, the 14-3-3ζ adopted a newly found wide-opened conformation. Based on our findings we additionally propose a secondary interaction site on the inner surface of the 14-3-3ζ dimer, and a direct interference on the binding process by the flexible C-terminal tail. A minimalistic model was designed to allow for the efficient calculation of absolute binding affinities. Binding affinities calculated from the potential of mean force along the binding pathway are in line with the available experimental estimates for two of the studied systems. PMID:28727767

A study of dynamic data placement for ATLAS distributed data management

NASA Astrophysics Data System (ADS)

Beermann, T.; Stewart, G. A.; Maettig, P.

2015-12-01

This contribution presents a study on the applicability and usefulness of dynamic data placement methods for data-intensive systems, such as ATLAS distributed data management (DDM). In this system the jobs are sent to the data, therefore having a good distribution of data is significant. Ways of forecasting workload patterns are examined which then are used to redistribute data to achieve a better overall utilisation of computing resources and to reduce waiting time for jobs before they can run on the grid. This method is based on a tracer infrastructure that is able to monitor and store historical data accesses and which is used to create popularity reports. These reports provide detailed summaries about data accesses in the past, including information about the accessed files, the involved users and the sites. From this past data it is possible to then make near-term forecasts for data popularity in the future. This study evaluates simple prediction methods as well as more complex methods like neural networks. Based on the outcome of the predictions a redistribution algorithm deletes unused replicas and adds new replicas for potentially popular datasets. Finally, a grid simulator is used to examine the effects of the redistribution. The simulator replays workload on different data distributions while measuring the job waiting time and site usage. The study examines how the average waiting time is affected by the amount of data that is moved, how it differs for the various forecasting methods and how that compares to the optimal data distribution.

Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations.

PubMed

Han, Nanyu; Mu, Yuguang

2013-01-01

Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147-150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus.

Plasticity of 150-Loop in Influenza Neuraminidase Explored by Hamiltonian Replica Exchange Molecular Dynamics Simulations

PubMed Central

Han, Nanyu; Mu, Yuguang

2013-01-01

Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147–150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus. PMID:23593372

Accuracy evaluation of intraoral optical impressions: A clinical study using a reference appliance.

PubMed

Atieh, Mohammad A; Ritter, André V; Ko, Ching-Chang; Duqum, Ibrahim

2017-09-01

Trueness and precision are used to evaluate the accuracy of intraoral optical impressions. Although the in vivo precision of intraoral optical impressions has been reported, in vivo trueness has not been evaluated because of limitations in the available protocols. The purpose of this clinical study was to compare the accuracy (trueness and precision) of optical and conventional impressions by using a novel study design. Five study participants consented and were enrolled. For each participant, optical and conventional (vinylsiloxanether) impressions of a custom-made intraoral Co-Cr alloy reference appliance fitted to the mandibular arch were obtained by 1 operator. Three-dimensional (3D) digital models were created for stone casts obtained from the conventional impression group and for the reference appliances by using a validated high-accuracy reference scanner. For the optical impression group, 3D digital models were obtained directly from the intraoral scans. The total mean trueness of each impression system was calculated by averaging the mean absolute deviations of the impression replicates from their 3D reference model for each participant, followed by averaging the obtained values across all participants. The total mean precision for each impression system was calculated by averaging the mean absolute deviations between all the impression replicas for each participant (10 pairs), followed by averaging the obtained values across all participants. Data were analyzed using repeated measures ANOVA (α=.05), first to assess whether a systematic difference in trueness or precision of replicate impressions could be found among participants and second to assess whether the mean trueness and precision values differed between the 2 impression systems. Statistically significant differences were found between the 2 impression systems for both mean trueness (P=.010) and mean precision (P=.007). Conventional impressions had higher accuracy with a mean trueness of 17.0 ±6.6 μm and mean precision of 16.9 ±5.8 μm than optical impressions with a mean trueness of 46.2 ±11.4 μm and mean precision of 61.1 ±4.9 μm. Complete arch (first molar-to-first molar) optical impressions were less accurate than conventional impressions but may be adequate for quadrant impressions. Copyright © 2016 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

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.

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

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).

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

2008-06-01

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A˚ Cα RMSD away from the experimentally determined structure.

Replica analysis of overfitting in regression models for time-to-event data

NASA Astrophysics Data System (ADS)

Coolen, A. C. C.; Barrett, J. E.; Paga, P.; Perez-Vicente, C. J.

2017-09-01

Overfitting, which happens when the number of parameters in a model is too large compared to the number of data points available for determining these parameters, is a serious and growing problem in survival analysis. While modern medicine presents us with data of unprecedented dimensionality, these data cannot yet be used effectively for clinical outcome prediction. Standard error measures in maximum likelihood regression, such as p-values and z-scores, are blind to overfitting, and even for Cox’s proportional hazards model (the main tool of medical statisticians), one finds in literature only rules of thumb on the number of samples required to avoid overfitting. In this paper we present a mathematical theory of overfitting in regression models for time-to-event data, which aims to increase our quantitative understanding of the problem and provide practical tools with which to correct regression outcomes for the impact of overfitting. It is based on the replica method, a statistical mechanical technique for the analysis of heterogeneous many-variable systems that has been used successfully for several decades in physics, biology, and computer science, but not yet in medical statistics. We develop the theory initially for arbitrary regression models for time-to-event data, and verify its predictions in detail for the popular Cox model.

Accelerating the Conformational Sampling of Intrinsically Disordered Proteins.

PubMed

Do, Trang Nhu; Choy, Wing-Yiu; Karttunen, Mikko

2014-11-11

Intrinsically disordered proteins (IDPs) are a class of proteins lacking a well-defined secondary structure. Instead, they are able to attain multiple conformations, bind to multiple targets, and respond to changes in their surroundings. Functionally, IDPs have been associated with molecular recognition, cell regulation, and signal transduction. The dynamic conformational ensemble of IDPs is highly environmental and binding partner dependent, rendering the characterization of IDPs extremely challenging. Here, we compare the sampling efficiencies of conventional molecular dynamics (MD), well-tempered metadynamics (WT-META), and bias-exchange metadynamics (BE-META). The total simulation time was over 10 μs, and a 20-mer peptide derived from the Neh2 domain of the Nuclear factor erythroid 2-related factor 2 (Nrf2) protein was simulated. BE-META, with a neutral replica and seven biased replicas employing a set of seven relevant collective variables (CVs), provided the most reliable and efficient sampling. Finally, we propose a free-energy reconstruction method based on the probability distribution of the secondary structure contents. This postprocessing analysis confirms the presence of not only the β-hairpin conformation of the free Neh2 peptide but also its rare bound-state-like conformation, both of that have been experimentally observed. In addition, our simulations also predict other possible conformations to be verified with future experiments.

Temperature-induced unfolding of epidermal growth factor (EGF): insight from molecular dynamics simulation

PubMed Central

Yan, Chunli; Pattani, Varun; Tunnell, James W.; Ren, Pengyu

2010-01-01

Thermal disruption of protein structure and function is a potentially powerful therapeutic vehicle. With the emerging nanoparticle-targeting and femtosecond laser technology, it is possible to deliver heating locally to specific molecules. It is therefore important to understand how fast a protein can unfold or lose its function at high temperatures, such as near the water boiling point. In this study, the thermal damage of EGF was investigated by combining the replica exchange (136 replicas) and conventional molecular dynamics simulations. The REMD simulation was employed to rigorously explore the free energy landscape of EGF unfolding. Interestingly, besides the native and unfolded states, we also observed a distinct molten globule (MG) state that retained substantial amount of native contacts. Based on the understanding that which the unfolding of EGF is a three-state process, we have examined the unfolding kinetics of EGF (N→ MG→h multiple 20-ns conventional MD simulations. The Arrhenius prefactors and activation energy barriers determined from the simulation are within the range of previously studied proteins. In contrast to the thermal damage of cells and tissues which take place on the time scale of seconds to hours at relatively low temperatures, the denaturation of proteins occur in nanoseconds when the temperature of heat bath approaches the boiling point. PMID:20466569

Comparative Study on Prediction Effects of Short Fatigue Crack Propagation Rate by Two Different Calculation Methods

NASA Astrophysics Data System (ADS)

Yang, Bing; Liao, Zhen; Qin, Yahang; Wu, Yayun; Liang, Sai; Xiao, Shoune; Yang, Guangwu; Zhu, Tao

2017-05-01

To describe the complicated nonlinear process of the fatigue short crack evolution behavior, especially the change of the crack propagation rate, two different calculation methods are applied. The dominant effective short fatigue crack propagation rates are calculated based on the replica fatigue short crack test with nine smooth funnel-shaped specimens and the observation of the replica films according to the effective short fatigue cracks principle. Due to the fast decay and the nonlinear approximation ability of wavelet analysis, the self-learning ability of neural network, and the macroscopic searching and global optimization of genetic algorithm, the genetic wavelet neural network can reflect the implicit complex nonlinear relationship when considering multi-influencing factors synthetically. The effective short fatigue cracks and the dominant effective short fatigue crack are simulated and compared by the Genetic Wavelet Neural Network. The simulation results show that Genetic Wavelet Neural Network is a rational and available method for studying the evolution behavior of fatigue short crack propagation rate. Meanwhile, a traditional data fitting method for a short crack growth model is also utilized for fitting the test data. It is reasonable and applicable for predicting the growth rate. Finally, the reason for the difference between the prediction effects by these two methods is interpreted.

Theory of adsorption in a polydisperse templated porous material: Hard sphere systems

NASA Astrophysics Data System (ADS)

RŻysko, Wojciech; Sokołowski, Stefan; Pizio, Orest

2002-03-01

A theoretical description of adsorption in a templated porous material, formed by an equilibrium quench of a polydisperse fluid composed of matrix and template particles and subsequent removal of the template particles is presented. The approach is based on the solution of the replica Ornstein-Zernike equations with Percus-Yevick and hypernetted chain closures. The method of solution uses expansions of size-dependent correlation functions into Fourier series, as described by Lado [J. Chem. Phys. 108, 6441 (1998)]. Specific calculations have been carried out for model systems, composed of hard spheres.

Binary logic based purely on Fresnel diffraction

NASA Astrophysics Data System (ADS)

Hamam, H.; de Bougrenet de La Tocnaye, J. L.

1995-09-01

Binary logic operations on two-dimensional data arrays are achieved by use of the self-imaging properties of Fresnel diffraction. The fields diffracted by periodic objects can be considered as the superimposition of weighted and shifted replicas of original objects. We show that a particular spatial organization of the input data can result in logical operations being performed on these data in the considered diffraction planes. Among various advantages, this approach is shown to allow the implementation of dual-track, nondissipative logical operators. Image algebra is presented as an experimental illustration of this principle.

Variability in Room Temperature Fatigue Life of Alpha+Beta Processed Ti-6Al-4V (Preprint)

DTIC Science & Technology

2008-10-01

approaches proposed by Magnusen et al. [ 4 ], Chan et al. [5], Tryon et al. [ 6 ], Laz et al. [7], and Jha et al. [8-9]. Based on extensive...stresses at several depths into the surface of the gauge section of the specimens. Layer removal was accomplished by electropolishing a   2c a 6 ...replicas taken including 6 at 675 MPa and 1 at 635 MPa. The number of crack measurements per test ranged from 1 to 9, but 4 was the most common. The

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.

NASA's Webb "Pathfinder Telescope" Successfully Completes First Super-Cold Optical Test

NASA Image and Video Library

2017-12-08

Testing is crucial part of NASA's success on Earth and in space. So, as the actual flight components of NASA's James Webb Space Telescope come together, engineers are testing the non-flight equipment to ensure that tests on the real Webb telescope later goes safely and according to plan. Recently, the "pathfinder telescope," or just “Pathfinder,” completed its first super-cold optical test that resulted in many first-of-a-kind demonstrations. "This test is the first dry-run of the equipment and procedures we will use to conduct an end-to-end optical test of the flight telescope and instruments," said Mark Clampin, Webb telescope Observatory Project Scientist at NASA's Goddard Space Flight Center in Greenbelt, Maryland. "It provides confidence that once the flight telescope is ready, we are fully prepared for a successful test of the flight hardware." The Pathfinder is a non-flight replica of the Webb telescope’s center section backplane, or “backbone,” that includes mirrors. The flight backplane comes in three segments, a center section and two wing-like parts, all of which will support large hexagonal mirrors on the Webb telescope. The pathfinder only consists of the center part of the backplane. However, during the test, it held two full size spare primary mirror segments and a full size spare secondary mirror to demonstrate the ability to optically test and align the telescope at the planned operating temperatures of -400 degrees Fahrenheit (-240 Celsius). Read more: www.nasa.gov/feature/goddard/nasas-webb-pathfinder-telesc... Credit: NASA/Goddard/Chris Gunn NASA image use policy. NASA Goddard Space Flight Center enables NASA’s mission through four scientific endeavors: Earth Science, Heliophysics, Solar System Exploration, and Astrophysics. Goddard plays a leading role in NASA’s accomplishments by contributing compelling scientific knowledge to advance the Agency’s mission. Follow us on Twitter Like us on Facebook Find us on Instagram

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.

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.

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.

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

Partitioning a macroscopic system into independent subsystems

NASA Astrophysics Data System (ADS)

Delle Site, Luigi; Ciccotti, Giovanni; Hartmann, Carsten

2017-08-01

We discuss the problem of partitioning a macroscopic system into a collection of independent subsystems. The partitioning of a system into replica-like subsystems is nowadays a subject of major interest in several fields of theoretical and applied physics. The thermodynamic approach currently favoured by practitioners is based on a phenomenological definition of an interface energy associated with the partition, due to a lack of easily computable expressions for a microscopic (i.e. particle-based) interface energy. In this article, we outline a general approach to derive sharp and computable bounds for the interface free energy in terms of microscopic statistical quantities. We discuss potential applications in nanothermodynamics and outline possible future directions.

Monolithic microfabricated valves and pumps by multilayer soft lithography.

PubMed

Unger, M A; Chou, H P; Thorsen, T; Scherer, A; Quake, S R

2000-04-07

Soft lithography is an alternative to silicon-based micromachining that uses replica molding of nontraditional elastomeric materials to fabricate stamps and microfluidic channels. We describe here an extension to the soft lithography paradigm, multilayer soft lithography, with which devices consisting of multiple layers may be fabricated from soft materials. We used this technique to build active microfluidic systems containing on-off valves, switching valves, and pumps entirely out of elastomer. The softness of these materials allows the device areas to be reduced by more than two orders of magnitude compared with silicon-based devices. The other advantages of soft lithography, such as rapid prototyping, ease of fabrication, and biocompatibility, are retained.

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

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.

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.

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.

3D printing of an aortic aneurysm to facilitate decision making and device selection for endovascular aneurysm repair in complex neck anatomy.

PubMed

Tam, Matthew D B S; Laycock, Stephen D; Brown, James R I; Jakeways, Matthew

2013-12-01

To describe rapid prototyping or 3-dimensional (3D) printing of aneurysms with complex neck anatomy to facilitate endovascular aneurysm repair (EVAR). A 75-year-old man had a 6.6-cm infrarenal aortic aneurysm that appeared on computed tomographic angiography to have a sharp neck angulation of ~90°. However, although the computed tomography (CT) data were analyzed using centerline of flow, the true neck length and relations of the ostial origins were difficult to determine. No multidisciplinary consensus could be reached as to which stent-graft to use owing to these borderline features of the neck anatomy. Based on past experience with rapid prototyping technology, a decision was taken to print a model of the aneurysm to aid in visualization of the neck anatomy. The CT data were segmented, processed, and converted into a stereolithographic format representing the lumen as a 3D volume, from which a full-sized replica was printed within 24 hours. The model demonstrated that the neck was adequate for stent-graft repair using the Aorfix device. Rapid prototyping of aortic aneurysms is feasible and can aid decision making and device delivery. Further work is required to test the value of 3D replicas in planning procedures and their impact on procedure time, radiation dose, and procedure cost.

Skin microrelief as a diagnostic tool (Conference Presentation)

NASA Astrophysics Data System (ADS)

Tchvialeva, Lioudmila; Phillips, Jamie; Zeng, Haishan; McLean, David; Lui, Harvey; Lee, Tim K.

2017-02-01

Skin surface roughness is an important property for differentiating skin diseases. Recently, roughness has also been identified as a potential diagnostic indicator in the early detection of skin cancer. Objective quantification is usually carried out by creating silicone replicas of the skin and then measuring the replicas. We have developed an alternative in-vivo technique to measure skin roughness based on laser speckle. Laser speckle is the interference pattern produced when coherent light is used to illuminate a rough surface and the backscattered light is imaged. Acquiring speckle contrast measurements from skin phantoms with controllable roughness, we created a calibration curve by linearly interpolating between measured points. This calibration curve accounts for internal scattering and is designed to evaluate skin microrelief whose root-mean-square roughness is in the range of 10-60 micrometers. To validate the effectiveness of our technique, we conducted a study to measure 243 skin lesions including actinic keratosis (8), basal cell carcinoma (24), malignant melanoma (31), nevus (73), squamous cell carcinoma (19), and seborrheic keratosis (79). The average roughness values ranged from 26 to 57 micrometers. Malignant melanoma was ranked as the smoothest and squamous cell carcinoma as the roughest lesion. An ANOVA test confirmed that malignant melanoma has significantly smaller roughness than other lesion types. Our results suggest that skin microrelief can be used to detect malignant melanoma from other skin conditions.

Replicas in Cultural Heritage: 3d Printing and the Museum Experience

NASA Astrophysics Data System (ADS)

Ballarin, M.; Balletti, C.; Vernier, P.

2018-05-01

3D printing has seen a recent massive diffusion for several applications, not least the field of Cultural Heritage. Being used for different purposes, such as study, analysis, conservation or access in museum exhibitions, 3D printed replicas need to undergo a process of validation also in terms of metrical precision and accuracy. The Laboratory of Photogrammetry of Iuav University of Venice has started several collaborations with Italian museum institutions firstly for the digital acquisition and then for the physical reproduction of objects of historical and artistic interest. The aim of the research is to analyse the metric characteristics of the printed model in relation to the original data, and to optimize the process that from the survey leads to the physical representation of an object. In fact, this could be acquired through different methodologies that have different precisions (multi-image photogrammetry, TOF laser scanner, triangulation based laser scanner), and it always involves a long processing phase. It should not be forgotten that the digital data have to undergo a series of simplifications, which, on one hand, eliminate the noise introduced by the acquisition process, but on the other one, they can lead to discrepancies between the physical copy and the original geometry. In this paper we will show the results obtained on a small archaeological find that was acquired and reproduced for a museum exhibition intended for blind and partially sighted people.

Experimental Validation of Plastic Mandible Models Produced by a "Low-Cost" 3-Dimensional Fused Deposition Modeling Printer.

PubMed

Maschio, Federico; Pandya, Mirali; Olszewski, Raphael

2016-03-22

The objective of this study was to investigate the accuracy of 3-dimensional (3D) plastic (ABS) models generated using a low-cost 3D fused deposition modelling printer. Two human dry mandibles were scanned with a cone beam computed tomography (CBCT) Accuitomo device. Preprocessing consisted of 3D reconstruction with Maxilim software and STL file repair with Netfabb software. Then, the data were used to print 2 plastic replicas with a low-cost 3D fused deposition modeling printer (Up plus 2®). Two independent observers performed the identification of 26 anatomic landmarks on the 4 mandibles (2 dry and 2 replicas) with a 3D measuring arm. Each observer repeated the identifications 20 times. The comparison between the dry and plastic mandibles was based on 13 distances: 8 distances less than 12 mm and 5 distances greater than 12 mm. The mean absolute difference (MAD) was 0.37 mm, and the mean dimensional error (MDE) was 3.76%. The MDE decreased to 0.93% for distances greater than 12 mm. Plastic models generated using the low-cost 3D printer UPplus2® provide dimensional accuracies comparable to other well-established rapid prototyping technologies. Validated low-cost 3D printers could represent a step toward the better accessibility of rapid prototyping technologies in the medical field.

An Evaluation of the Gap Sizes of 3-Unit Fixed Dental Prostheses Milled from Sintering Metal Blocks.

PubMed

Jung, Jae-Kwan

2017-01-01

This study assessed the clinical acceptability of sintering metal-fabricated 3-unit fixed dental prostheses (FDPs) based on gap sizes. Ten specimens were prepared on research models by milling sintering metal blocks or by the lost-wax technique (LWC group). Gap sizes were assessed at 12 points per abutment (premolar and molar), 24 points per specimen (480 points in a total in 20 specimens). The measured points were categorized as marginal, axial wall, and occlusal for assessment in a silicone replica. The silicone replica was cut through the mesiodistal and buccolingual center. The four sections were magnified at 160x, and the thickness of the light body silicone was measured to determine the gap size, and gap size means were compared. For the premolar part, the mean (standard deviation) gap size was nonsignificantly ( p = 0.139) smaller in the SMB group (68.6 ± 35.6  μ m) than in the LWC group (69.6 ± 16.9  μ m). The mean molar gap was nonsignificantly smaller ( p = 0.852) in the LWC (73.9 ± 25.6  μ m) than in the SMB (78.1 ± 37.4  μ m) group. The gap sizes were similar between the two groups. Because the gap sizes were within the previously proposed clinically accepted limit, FDPs prepared by sintered metal block milling are clinically acceptable.

An Evaluation of the Gap Sizes of 3-Unit Fixed Dental Prostheses Milled from Sintering Metal Blocks

PubMed Central

2017-01-01

This study assessed the clinical acceptability of sintering metal-fabricated 3-unit fixed dental prostheses (FDPs) based on gap sizes. Ten specimens were prepared on research models by milling sintering metal blocks or by the lost-wax technique (LWC group). Gap sizes were assessed at 12 points per abutment (premolar and molar), 24 points per specimen (480 points in a total in 20 specimens). The measured points were categorized as marginal, axial wall, and occlusal for assessment in a silicone replica. The silicone replica was cut through the mesiodistal and buccolingual center. The four sections were magnified at 160x, and the thickness of the light body silicone was measured to determine the gap size, and gap size means were compared. For the premolar part, the mean (standard deviation) gap size was nonsignificantly (p = 0.139) smaller in the SMB group (68.6 ± 35.6 μm) than in the LWC group (69.6 ± 16.9 μm). The mean molar gap was nonsignificantly smaller (p = 0.852) in the LWC (73.9 ± 25.6 μm) than in the SMB (78.1 ± 37.4 μm) group. The gap sizes were similar between the two groups. Because the gap sizes were within the previously proposed clinically accepted limit, FDPs prepared by sintered metal block milling are clinically acceptable. PMID:28246605

Bioelectrochemical Detection of Mycobacterium tuberculosis ESAT-6 in an Antibody-Based Biomicrosystem

PubMed Central

Sepulveda, Danna; Varela, Andres; Del Portillo, Patricia

2017-01-01

Bioelectrochemical sensing of Mycobacterium tuberculosis through electro-immunosensors is a promising technique to detect relevant analytes. In general, immunosensors require the formation of organic assemblies by the adsorption of molecular constituents. Moreover, they depend on the correct immobilization of the bio-recognition element in the biosensor. These procedures cannot be easily monitored without the use of invasive methods. In this work, an impedance analysis technique was used, as a non-invasive method, to measure and differentiate the manufacturing stages of the sensors. Biomicrosystems were fabricated through physical vapor deposition (PVD) of 80 nm Au nanolayers on 35 µm copper surfaces. Later, the surface was modified through thiolation methods generating a self-assembled-monolayer (SAM) with 20 mM 4-aminothiophenol (4-ATP) on which a polyclonal antibody (pAb) was covalently attached. Using impedance analysis, every step of the electro-immunosensor fabrication protocol was characterized using 40 independent replicas. Results showed that, compared to the negative controls, distilled water, and 0.5 µg/mL HSA, a maximum variation of 171% between each replica was achieved when compared to samples containing 0.5 µg/mL of ESAT-6 M. tuberculosis immunodominant protein. Therefore, this development validates a non-invasive method to electrically monitor the assembly process of electro-immunosensors and a tool for its further measure for detection of relevant antigens. PMID:28937645

Experimental Validation of Plastic Mandible Models Produced by a “Low-Cost” 3-Dimensional Fused Deposition Modeling Printer

PubMed Central

Maschio, Federico; Pandya, Mirali; Olszewski, Raphael

2016-01-01

Background The objective of this study was to investigate the accuracy of 3-dimensional (3D) plastic (ABS) models generated using a low-cost 3D fused deposition modelling printer. Material/Methods Two human dry mandibles were scanned with a cone beam computed tomography (CBCT) Accuitomo device. Preprocessing consisted of 3D reconstruction with Maxilim software and STL file repair with Netfabb software. Then, the data were used to print 2 plastic replicas with a low-cost 3D fused deposition modeling printer (Up plus 2®). Two independent observers performed the identification of 26 anatomic landmarks on the 4 mandibles (2 dry and 2 replicas) with a 3D measuring arm. Each observer repeated the identifications 20 times. The comparison between the dry and plastic mandibles was based on 13 distances: 8 distances less than 12 mm and 5 distances greater than 12 mm. Results The mean absolute difference (MAD) was 0.37 mm, and the mean dimensional error (MDE) was 3.76%. The MDE decreased to 0.93% for distances greater than 12 mm. Conclusions Plastic models generated using the low-cost 3D printer UPplus2® provide dimensional accuracies comparable to other well-established rapid prototyping technologies. Validated low-cost 3D printers could represent a step toward the better accessibility of rapid prototyping technologies in the medical field. PMID:27003456

Real-time analysis keratometer

NASA Technical Reports Server (NTRS)

Adachi, Iwao P. (Inventor); Adachi, Yoshifumi (Inventor); Frazer, Robert E. (Inventor)

1987-01-01

A computer assisted keratometer in which a fiducial line pattern reticle illuminated by CW or pulsed laser light is projected on a corneal surface through lenses, a prismoidal beamsplitter quarterwave plate, and objective optics. The reticle surface is curved as a conjugate of an ideal corneal curvature. The fiducial image reflected from the cornea undergoes a polarization shift through the quarterwave plate and beamsplitter whereby the projected and reflected beams are separated and directed orthogonally. The reflected beam fiducial pattern forms a moire pattern with a replica of the first recticle. This moire pattern contains transverse aberration due to differences in curvature between the cornea and the ideal corneal curvature. The moire pattern is analyzed in real time by computer which displays either the CW moire pattern or a pulsed mode analysis of the transverse aberration of the cornea under observation, in real time. With the eye focused on a plurality of fixation points in succession, a survey of the entire corneal topography is made and a contour map or three dimensional plot of the cornea can be made as a computer readout in addition to corneal radius and refractive power analysis.

Response of resin transfer molded (RTM) composites under reversed cyclic loading

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

Mahfuz, H.; Haque, A.; Yu, D.

1996-01-01

Compressive behavior and the tension-compression fatigue response of resin transfer molded IM7 PW/PR 500 composite laminate with a circular notch have been studied. Fatigue damage characteristics have been investigated through the changes in the laminate strength and stiffness by gradually incrementing the fatigue cycles at a preselected load level. Progressive damage in the surface of the laminate during fatigue has been investigated using cellulose replicas. Failure mechanisms during static and cyclic tests have been identified and presented in detail. Extensive debonding of filaments and complete fiber bundle fracture accompanied by delamination were found to be responsible for fatigue failures, whilemore » fiber buckling, partial fiber fracture and delamination were characterized as the failure modes during static tests. Weibull analysis of the static, cyclic and residual tests have been performed and described in detail. Fractured as well as untested specimens were C-scanned, and the progressive damage growth during fatigue is presented. Optical Microscopy (OM) and Scanning Electron Microscopy (SEM) for the fractured specimen were also performed and the analysis of the failure behavior is presented.« less

On the identification of folium and orchil on illuminated manuscripts.

PubMed

Aceto, Maurizio; Calà, Elisa; Agostino, Angelo; Fenoglio, Gaia; Idone, Ambra; Porter, Cheryl; Gulmini, Monica

2017-01-15

The identification of the two purple dyes folium and orchil has rarely been reported in the analysis of painted artworks, especially when analysing illuminated manuscripts. This is not consistent with the fact that ancient literary sources suggested their use as substitutes for the more expensive Tyrian purple dye. By employing non-invasive spectroscopic techniques, the present work demonstrates that these dyes were actually widely used in the production of ancient manuscripts. By employing UV-visible diffuse reflectance spectrophotometry with optic fibres (FORS) and spectrofluorimetry, the abundant identification of both dyes on medieval manuscripts was performed by comparing the spectra recorded on ancient codices with those obtained on accurate replicas of dyed or painted parchment. Moreover, examples are also reported whereby the considered purple dyes were used in mixtures with other colourants. The overall information obtained here allowed us to define new boundaries for the time range in which orchil and folium dyes were used which is wider than previously thought, and to focus on their particular uses in the decoration of books. Copyright © 2016 Elsevier B.V. All rights reserved.

Enhanced sampling simulation analysis of the structure of lignin in the THF–water miscibility gap

DOE PAGES

Smith, Micholas Dean; Petridis, Loukas; Cheng, Xiaolin; ...

2016-01-26

Using temperature replica-exchange molecular dynamics, we characterize a globule-to-coil transition for a softwood-like lignin biopolymer in a tetrahydrofuran (THF)-water cosolvent system at temperatures at which the cosolvent undergoes a de-mixing transition. The lignin is found to be in a coil state, similar to that in the high-temperature miscible region. Analysis of the transition kinetics indicates that THF acts in a surfactant-like fashion. In conclusion, the present study thus suggests that THF-water based pretreatments may efficiently remove lignin from biomass even at relatively low (non-water boiling) temperatures.

Polymer blend lithography for metal films: large-area patterning with over 1 billion holes/inch(2).

PubMed

Huang, Cheng; Förste, Alexander; Walheim, Stefan; Schimmel, Thomas

2015-01-01

Polymer blend lithography (PBL) is a spin-coating-based technique that makes use of the purely lateral phase separation between two immiscible polymers to fabricate large area nanoscale patterns. In our earlier work (Huang et al. 2012), PBL was demonstrated for the fabrication of patterned self-assembled monolayers. Here, we report a new method based on the technique of polymer blend lithography that allows for the fabrication of metal island arrays or perforated metal films on the nanometer scale, the metal PBL. As the polymer blend system in this work, a mixture of polystyrene (PS) and poly(methyl methacrylate) (PMMA), dissolved in methyl ethyl ketone (MEK) is used. This system forms a purely lateral structure on the substrate at controlled humidity, which means that PS droplets are formed in a PMMA matrix, whereby both phases have direct contact both to the substrate and to the air interface. Therefore, a subsequent selective dissolution of either the PS or PMMA component leaves behind a nanostructured film which can be used as a lithographic mask. We use this lithographic mask for the fabrication of metal patterns by thermal evaporation of the metal, followed by a lift-off process. As a consequence, the resulting metal nanostructure is an exact replica of the pattern of the selectively removed polymer (either a perforated metal film or metal islands). The minimum diameter of these holes or metal islands demonstrated here is about 50 nm. Au, Pd, Cu, Cr and Al templates were fabricated in this work by metal PBL. The wavelength-selective optical transmission spectra due to the localized surface plasmonic effect of the holes in perforated Al films were investigated and compared to the respective hole diameter histograms.

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

Precision of fit between implant impression coping and implant replica pairs for three implant systems.

PubMed

Nicoll, Roxanna J; Sun, Albert; Haney, Stephan; Turkyilmaz, Ilser

2013-01-01

The fabrication of an accurately fitting implant-supported fixed prosthesis requires multiple steps, the first of which is assembling the impression coping on the implant. An imprecise fit of the impression coping on the implant will cause errors that will be magnified in subsequent steps of prosthesis fabrication. The purpose of this study was to characterize the 3-dimensional (3D) precision of fit between impression coping and implant replica pairs for 3 implant systems. The selected implant systems represent the 3 main joint types used in implant dentistry: external hexagonal, internal trilobe, and internal conical. Ten impression copings and 10 implant replicas from each of the 3 systems, B (Brånemark System), R (NobelReplace Select), and A (NobelActive) were paired. A standardized aluminum test body was luted to each impression coping, and the corresponding implant replica was embedded in a stone base. A coordinate measuring machine was used to quantify the maximum range of displacement in a vertical direction as a function of the tightening force applied to the guide pin. Maximum angular displacement in a horizontal plane was measured as a function of manual clockwise or counterclockwise rotation. Vertical and rotational positioning was analyzed by using 1-way analysis of variance (ANOVA). The Fisher protected least significant difference (PLSD) multiple comparisons test of the means was applied when the F-test in the ANOVA was significant (α=.05). The mean and standard deviation for change in the vertical positioning of impression copings was 4.3 ±2.1 μm for implant system B, 2.8 ±4.2 μm for implant system R, and 20.6 ±8.8 μm for implant system A. The mean and standard deviation for rotational positioning was 3.21 ±0.98 degrees for system B, 2.58 ±1.03 degrees for system R, and 5.30 ±0.79 degrees for system A. The P-value for vertical positioning between groups A and B and between groups A and R was <.001. No significant differences were found for vertical positioning between groups B and R. The P-value for rotational positioning between groups A and B and between groups A and R was <.001. No significant differences were found for rotational positioning between groups B and R. The results of the study confirmed that implant systems differ in precision of fit. Vertical precision between paired implant components is a function of joint type and the tightening force applied to the guide pin. The magnitude of vertical displacement with applied torque is greater for conical connections than for butt joint connections. The rotational freedom between paired components is unique to the implant system and is presumably related to the machining tolerances specified by the manufacturer. Copyright © 2013 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

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.