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.

Enhanced Conformational Sampling in Molecular Dynamics Simulations of Solvated Peptides: Fragment-Based Local Elevation Umbrella Sampling.

PubMed

Hansen, Halvor S; Daura, Xavier; Hünenberger, Philippe H

2010-09-14

A new method, fragment-based local elevation umbrella sampling (FB-LEUS), is proposed to enhance the conformational sampling in explicit-solvent molecular dynamics (MD) simulations of solvated polymers. The method is derived from the local elevation umbrella sampling (LEUS) method [ Hansen and Hünenberger , J. Comput. Chem. 2010 , 31 , 1 - 23 ], which combines the local elevation (LE) conformational searching and the umbrella sampling (US) conformational sampling approaches into a single scheme. In LEUS, an initial (relatively short) LE build-up (searching) phase is used to construct an optimized (grid-based) biasing potential within a subspace of conformationally relevant degrees of freedom, which is then frozen and used in a (comparatively longer) US sampling phase. This combination dramatically enhances the sampling power of MD simulations but, due to computational and memory costs, is only applicable to relevant subspaces of low dimensionalities. As an attempt to expand the scope of the LEUS approach to solvated polymers with more than a few relevant degrees of freedom, the FB-LEUS scheme involves an US sampling phase that relies on a superposition of low-dimensionality biasing potentials optimized using LEUS at the fragment level. The feasibility of this approach is tested using polyalanine (poly-Ala) and polyvaline (poly-Val) oligopeptides. Two-dimensional biasing potentials are preoptimized at the monopeptide level, and subsequently applied to all dihedral-angle pairs within oligopeptides of 4,  6,  8, or 10 residues. Two types of fragment-based biasing potentials are distinguished: (i) the basin-filling (BF) potentials act so as to "fill" free-energy basins up to a prescribed free-energy level above the global minimum; (ii) the valley-digging (VD) potentials act so as to "dig" valleys between the (four) free-energy minima of the two-dimensional maps, preserving barriers (relative to linearly interpolated free-energy changes) of a prescribed magnitude

Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling.

PubMed

Yang, Yi Isaac; Parrinello, Michele

2018-06-12

Collective variables are used often in many enhanced sampling methods, and their choice is a crucial factor in determining sampling efficiency. However, at times, searching for good collective variables can be challenging. In a recent paper, we combined time-lagged independent component analysis with well-tempered metadynamics in order to obtain improved collective variables from metadynamics runs that use lower quality collective variables [ McCarty, J.; Parrinello, M. J. Chem. Phys. 2017 , 147 , 204109 ]. In this work, we extend these ideas to variationally enhanced sampling. This leads to an efficient scheme that is able to make use of the many advantages of the variational scheme. We apply the method to alanine-3 in water. From an alanine-3 variationally enhanced sampling trajectory in which all the six dihedral angles are biased, we extract much better collective variables able to describe in exquisite detail the protein complex free energy surface in a low dimensional representation. The success of this investigation is helped by a more accurate way of calculating the correlation functions needed in the time-lagged independent component analysis and from the introduction of a new basis set to describe the dihedral angles arrangement.

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.

PubMed

Miao, Yinglong; Feher, Victoria A; McCammon, J Andrew

2015-08-11

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding, and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low-energy states of the biomolecules and characterize the protein-folding and ligand-binding pathways quantitatively.

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

PubMed

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

2015-05-01

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

Self-adaptive enhanced sampling in the energy and trajectory spaces: accelerated thermodynamics and kinetic calculations.

PubMed

Gao, Yi Qin

2008-04-07

Here, we introduce a simple self-adaptive computational method to enhance the sampling in energy, configuration, and trajectory spaces. The method makes use of two strategies. It first uses a non-Boltzmann distribution method to enhance the sampling in the phase space, in particular, in the configuration space. The application of this method leads to a broad energy distribution in a large energy range and a quickly converged sampling of molecular configurations. In the second stage of simulations, the configuration space of the system is divided into a number of small regions according to preselected collective coordinates. An enhanced sampling of reactive transition paths is then performed in a self-adaptive fashion to accelerate kinetics calculations.

Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation

PubMed Central

2016-01-01

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced sampling and free energy calculation of biomolecules is presented. By constructing a boost potential that follows Gaussian distribution, accurate reweighting of the GaMD simulations is achieved using cumulant expansion to the second order. Here, GaMD is demonstrated on three biomolecular model systems: alanine dipeptide, chignolin folding, and ligand binding to the T4-lysozyme. Without the need to set predefined reaction coordinates, GaMD enables unconstrained enhanced sampling of these biomolecules. Furthermore, the free energy profiles obtained from reweighting of the GaMD simulations allow us to identify distinct low-energy states of the biomolecules and characterize the protein-folding and ligand-binding pathways quantitatively. PMID:26300708

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

PubMed

Fujisaki, Hiroshi; Moritsugu, Kei; Matsunaga, Yasuhiro; Morishita, Tetsuya; Maragliano, Luca

2015-01-01

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD), Logarithmic Mean Force Dynamics (LogMFD), and Multiscale Enhanced Sampling (MSES) algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free-energy landscape via automatic exploration.

Enhancement of RNA from Formalin-Fixed Paraffin-Embedded (FFPE) Samples

EPA Science Inventory

Enhancement of RNA from Formalin-Fixed Paraffin-Embedded (FFPE) Samples Susan Hester1, Leah Wehmas1, Carole Yauk2, Marc Roy3, Mark M. Gosink3, Deidre D. Wilk4, Thomas Hill III5, Charles E. Wood11Office of Research and Development, US EPA, RTP, NC 27709, USA, 2Environmental Health...

History of Resistance Welding Oxide Dispersion Strengthened Cladding and other High Temperature Materials at Center for Advanced Energy Studies

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

Larry Zirker; Nathan Jerred; Dr. Indrajit Charit

2012-03-01

Research proposal 08-1079, 'A Comparative Study of Welded ODS Cladding Materials for AFCI/GNEP,' was funded in 2008 under an Advanced Fuel Cycle Initiative (AFCI) Research and Development Funding Opportunity, number DE-PS07-08ID14906. Th proposal sought to conduct research on joining oxide dispersion strengthen (ODS) tubing material to a solid end plug. This document summarizes the scientific and technical progress achieved during the project, which ran from 2008 to 2011.

Enhanced sampling simulations of DNA step parameters.

PubMed

Karolak, Aleksandra; van der Vaart, Arjan

2014-12-15

A novel approach for the selection of step parameters as reaction coordinates in enhanced sampling simulations of DNA is presented. The method uses three atoms per base and does not require coordinate overlays or idealized base pairs. This allowed for a highly efficient implementation of the calculation of all step parameters and their Cartesian derivatives in molecular dynamics simulations. Good correlation between the calculated and actual twist, roll, tilt, shift, and slide parameters is obtained, while the correlation with rise is modest. The method is illustrated by its application to the methylated and unmethylated 5'-CATGTGACGTCACATG-3' double stranded DNA sequence. One-dimensional umbrella simulations indicate that the flexibility of the central CG step is only marginally affected by methylation. © 2014 Wiley Periodicals, Inc.

Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems.

PubMed

Pan, Albert C; Weinreich, Thomas M; Piana, Stefano; Shaw, David E

2016-03-08

Molecular dynamics (MD) simulations can describe protein motions in atomic detail, but transitions between protein conformational states sometimes take place on time scales that are infeasible or very expensive to reach by direct simulation. Enhanced sampling methods, the aim of which is to increase the sampling efficiency of MD simulations, have thus been extensively employed. The effectiveness of such methods when applied to complex biological systems like proteins, however, has been difficult to establish because even enhanced sampling simulations of such systems do not typically reach time scales at which convergence is extensive enough to reliably quantify sampling efficiency. Here, we obtain sufficiently converged simulations of three proteins to evaluate the performance of simulated tempering, a member of a widely used class of enhanced sampling methods that use elevated temperature to accelerate sampling. Simulated tempering simulations with individual lengths of up to 100 μs were compared to (previously published) conventional MD simulations with individual lengths of up to 1 ms. With two proteins, BPTI and ubiquitin, we evaluated the efficiency of sampling of conformational states near the native state, and for the third, the villin headpiece, we examined the rate of folding and unfolding. Our comparisons demonstrate that simulated tempering can consistently achieve a substantial sampling speedup of an order of magnitude or more relative to conventional MD.

Antiferromagnetic Chern Insulators in Noncentrosymmetric Systems

NASA Astrophysics Data System (ADS)

Jiang, Kun; Zhou, Sen; Dai, Xi; Wang, Ziqiang

2018-04-01

We investigate a new class of topological antiferromagnetic (AF) Chern insulators driven by electronic interactions in two-dimensional systems without inversion symmetry. Despite the absence of a net magnetization, AF Chern insulators (AFCI) possess a nonzero Chern number C and exhibit the quantum anomalous Hall effect (QAHE). Their existence is guaranteed by the bifurcation of the boundary line of Weyl points between a quantum spin Hall insulator and a topologically trivial phase with the emergence of AF long-range order. As a concrete example, we study the phase structure of the honeycomb lattice Kane-Mele model as a function of the inversion-breaking ionic potential and the Hubbard interaction. We find an easy z axis C =1 AFCI phase and a spin-flop transition to a topologically trivial x y plane collinear antiferromagnet. We propose experimental realizations of the AFCI and QAHE in correlated electron materials and cold atom systems.

Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations.

PubMed

Harpole, Tyler J; Delemotte, Lucie

2018-04-01

The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscapes of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulations allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors. We focus on the various enhanced sampling techniques used to study these questions, how the conclusions come together to build a coherent picture, and the relationship between simulation outcomes and experimental observables. Copyright © 2017 Elsevier B.V. All rights reserved.

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

PubMed

König, Gerhard; Miller, Benjamin T; Boresch, Stefan; Wu, Xiongwu; Brooks, Bernard R

2012-10-09

One of the key requirements for the accurate calculation of free energy differences is proper sampling of conformational space. Especially in biological applications, molecular dynamics simulations are often confronted with rugged energy surfaces and high energy barriers, leading to insufficient sampling and, in turn, poor convergence of the free energy results. In this work, we address this problem by employing enhanced sampling methods. We explore the possibility of using self-guided Langevin dynamics (SGLD) to speed up the exploration process in free energy simulations. To obtain improved free energy differences from such simulations, it is necessary to account for the effects of the bias due to the guiding forces. We demonstrate how this can be accomplished for the Bennett's acceptance ratio (BAR) and the enveloping distribution sampling (EDS) methods. While BAR is considered among the most efficient methods available for free energy calculations, the EDS method developed by Christ and van Gunsteren is a promising development that reduces the computational costs of free energy calculations by simulating a single reference state. To evaluate the accuracy of both approaches in connection with enhanced sampling, EDS was implemented in CHARMM. For testing, we employ benchmark systems with analytical reference results and the mutation of alanine to serine. We find that SGLD with reweighting can provide accurate results for BAR and EDS where conventional molecular dynamics simulations fail. In addition, we compare the performance of EDS with other free energy methods. We briefly discuss the implications of our results and provide practical guidelines for conducting free energy simulations with SGLD.

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables.

PubMed

Hashemian, Behrooz; Millán, Daniel; Arroyo, Marino

2013-12-07

Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.

Modeling and enhanced sampling of molecular systems with smooth and nonlinear data-driven collective variables

NASA Astrophysics Data System (ADS)

Hashemian, Behrooz; Millán, Daniel; Arroyo, Marino

2013-12-01

Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability to automatically characterize molecular collective behavior. Unfortunately, these methods fail to provide a differentiable function mapping high-dimensional configurations to their low-dimensional representation, as required in enhanced sampling methods. We introduce a methodology that, starting from an ensemble representative of molecular flexibility, builds smooth and nonlinear data-driven collective variables (SandCV) from the output of nonlinear manifold learning algorithms. We demonstrate the method with a standard benchmark molecule, alanine dipeptide, and show how it can be non-intrusively combined with off-the-shelf enhanced sampling methods, here the adaptive biasing force method. We illustrate how enhanced sampling simulations with SandCV can explore regions that were poorly sampled in the original molecular ensemble. We further explore the transferability of SandCV from a simpler system, alanine dipeptide in vacuum, to a more complex system, alanine dipeptide in explicit water.

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.

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.

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

Exploring protein kinase conformation using swarm-enhanced sampling molecular dynamics.

PubMed

Atzori, Alessio; Bruce, Neil J; Burusco, Kepa K; Wroblowski, Berthold; Bonnet, Pascal; Bryce, Richard A

2014-10-27

Protein plasticity, while often linked to biological function, also provides opportunities for rational design of selective and potent inhibitors of their function. The application of computational methods to the prediction of concealed protein concavities is challenging, as the motions involved can be significant and occur over long time scales. Here we introduce the swarm-enhanced sampling molecular dynamics (sesMD) method as a tool to improve sampling of conformational landscapes. In this approach, a swarm of replica simulations interact cooperatively via a set of pairwise potentials incorporating attractive and repulsive components. We apply the sesMD approach to explore the conformations of the DFG motif in the protein p38α mitogen-activated protein kinase. In contrast to multiple MD simulations, sesMD trajectories sample a range of DFG conformations, some of which map onto existing crystal structures. Simulated structures intermediate between the DFG-in and DFG-out conformations are predicted to have druggable pockets of interest for structure-based ligand design.

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes.

PubMed

Higo, Junichi; Ikebe, Jinzen; Kamiya, Narutoshi; Nakamura, Haruki

2012-03-01

Protein folding and protein-ligand docking have long persisted as important subjects in biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic expressions, i.e., all-atom protein models and an explicit solvent, free-energy landscapes have been computed for several systems, such as the folding of peptides/proteins composed of a few amino acids up to nearly 60 amino-acid residues, protein-ligand interactions, and coupled folding and binding of intrinsically disordered proteins. Recent progress in conformational sampling and its applications to biophysical systems are reviewed in this report, including descriptions of several outstanding studies. In addition, an algorithm and detailed procedures used for multicanonical sampling are presented along with the methodology of adaptive umbrella sampling. Both methods control the simulation so that low-probability regions along a reaction coordinate are sampled frequently. The reaction coordinate is the potential energy for multicanonical sampling and is a structural identifier for adaptive umbrella sampling. One might imagine that this probability control invariably enhances conformational transitions among distinct stable states, but this study examines the enhanced conformational sampling of a simple system and shows that reasonably well-controlled sampling slows the transitions. This slowing is induced by a rapid change of entropy along the reaction coordinate. We then provide a recipe to speed up the sampling by loosening the rapid change of entropy. Finally, we report all-atom McMD simulation results of various biophysical systems in an explicit solvent.

Molecular dynamics based enhanced sampling of collective variables with very large time steps.

PubMed

Chen, Pei-Yang; Tuckerman, Mark E

2018-01-14

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

Molecular dynamics based enhanced sampling of collective variables with very large time steps

NASA Astrophysics Data System (ADS)

Chen, Pei-Yang; Tuckerman, Mark E.

2018-01-01

Enhanced sampling techniques that target a set of collective variables and that use molecular dynamics as the driving engine have seen widespread application in the computational molecular sciences as a means to explore the free-energy landscapes of complex systems. The use of molecular dynamics as the fundamental driver of the sampling requires the introduction of a time step whose magnitude is limited by the fastest motions in a system. While standard multiple time-stepping methods allow larger time steps to be employed for the slower and computationally more expensive forces, the maximum achievable increase in time step is limited by resonance phenomena, which inextricably couple fast and slow motions. Recently, we introduced deterministic and stochastic resonance-free multiple time step algorithms for molecular dynamics that solve this resonance problem and allow ten- to twenty-fold gains in the large time step compared to standard multiple time step algorithms [P. Minary et al., Phys. Rev. Lett. 93, 150201 (2004); B. Leimkuhler et al., Mol. Phys. 111, 3579-3594 (2013)]. These methods are based on the imposition of isokinetic constraints that couple the physical system to Nosé-Hoover chains or Nosé-Hoover Langevin schemes. In this paper, we show how to adapt these methods for collective variable-based enhanced sampling techniques, specifically adiabatic free-energy dynamics/temperature-accelerated molecular dynamics, unified free-energy dynamics, and by extension, metadynamics, thus allowing simulations employing these methods to employ similarly very large time steps. The combination of resonance-free multiple time step integrators with free-energy-based enhanced sampling significantly improves the efficiency of conformational exploration.

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.

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.

Influence of high-conductivity buffer composition on field-enhanced sample injection coupled to sweeping in CE.

PubMed

Anres, Philippe; Delaunay, Nathalie; Vial, Jérôme; Thormann, Wolfgang; Gareil, Pierre

2013-02-01

The aim of this work was to clarify the mechanism taking place in field-enhanced sample injection coupled to sweeping and micellar EKC (FESI-Sweep-MEKC), with the utilization of two acidic high-conductivity buffers (HCBs), phosphoric acid or sodium phosphate buffer, in view of maximizing sensitivity enhancements. Using cationic model compounds in acidic media, a chemometric approach and simulations with SIMUL5 were implemented. Experimental design first enabled to identify the significant factors and their potential interactions. Simulation demonstrates the formation of moving boundaries during sample injection, which originate at the initial sample/HCB and HCB/buffer discontinuities and gradually change the compositions of HCB and BGE. With sodium phosphate buffer, the HCB conductivity increased during the injection, leading to a more efficient preconcentration by staking (about 1.6 times) than with phosphoric acid alone, for which conductivity decreased during injection. For the same injection time at constant voltage, however, a lower amount of analytes was injected with sodium phosphate buffer than with phosphoric acid. Consequently sensitivity enhancements were lower for the whole FESI-Sweep-MEKC process. This is why, in order to maximize sensitivity enhancements, it is proposed to work with sodium phosphate buffer as HCB and to use constant current during sample injection. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhancement of low sampling frequency recordings for ECG biometric matching using interpolation.

PubMed

Sidek, Khairul Azami; Khalil, Ibrahim

2013-01-01

Electrocardiogram (ECG) based biometric matching suffers from high misclassification error with lower sampling frequency data. This situation may lead to an unreliable and vulnerable identity authentication process in high security applications. In this paper, quality enhancement techniques for ECG data with low sampling frequency has been proposed for person identification based on piecewise cubic Hermite interpolation (PCHIP) and piecewise cubic spline interpolation (SPLINE). A total of 70 ECG recordings from 4 different public ECG databases with 2 different sampling frequencies were applied for development and performance comparison purposes. An analytical method was used for feature extraction. The ECG recordings were segmented into two parts: the enrolment and recognition datasets. Three biometric matching methods, namely, Cross Correlation (CC), Percent Root-Mean-Square Deviation (PRD) and Wavelet Distance Measurement (WDM) were used for performance evaluation before and after applying interpolation techniques. Results of the experiments suggest that biometric matching with interpolated ECG data on average achieved higher matching percentage value of up to 4% for CC, 3% for PRD and 94% for WDM. These results are compared with the existing method when using ECG recordings with lower sampling frequency. Moreover, increasing the sample size from 56 to 70 subjects improves the results of the experiment by 4% for CC, 14.6% for PRD and 0.3% for WDM. Furthermore, higher classification accuracy of up to 99.1% for PCHIP and 99.2% for SPLINE with interpolated ECG data as compared of up to 97.2% without interpolation ECG data verifies the study claim that applying interpolation techniques enhances the quality of the ECG data. Crown Copyright © 2012. Published by Elsevier Ireland Ltd. All rights reserved.

Donor-Acceptor Distance Sampling Enhances the Performance of "Better than Nature" Nicotinamide Coenzyme Biomimetics.

PubMed

Geddes, Alexander; Paul, Caroline E; Hay, Sam; Hollmann, Frank; Scrutton, Nigel S

2016-09-07

Understanding the mechanisms of enzymatic hydride transfer with nicotinamide coenzyme biomimetics (NCBs) is critical to enhancing the performance of nicotinamide coenzyme-dependent biocatalysts. Here the temperature dependence of kinetic isotope effects (KIEs) for hydride transfer between "better than nature" NCBs and several ene reductase biocatalysts is used to indicate transfer by quantum mechanical tunneling. A strong correlation between rate constants and temperature dependence of the KIE (ΔΔH(⧧)) for H/D transfer implies that faster reactions with NCBs are associated with enhanced donor-acceptor distance sampling. Our analysis provides the first mechanistic insight into how NCBs can outperform their natural counterparts and emphasizes the need to optimize donor-acceptor distance sampling to obtain high catalytic performance from H-transfer enzymes.

Design of the sample cell in near-field surface-enhanced Raman scattering by finite difference time domain method

NASA Astrophysics Data System (ADS)

Li, Yaqin; Jian, Guoshu; Wu, Shifa

2006-11-01

The rational design of the sample cell may improve the sensitivity of surface-enhanced Raman scattering (SERS) detection in a high degree. Finite difference time domain (FDTD) simulations of the configuration of Ag film-Ag particles illuminated by plane wave and evanescent wave are performed to provide physical insight for design of the sample cell. Numerical solutions indicate that the sample cell can provide more "hot spots' and the massive field intensity enhancement occurs in these "hot spots'. More information on the nanometer character of the sample can be got because of gradient-field Raman (GFR) of evanescent wave.

Free energy landscapes of peptides by enhanced conformational sampling.

PubMed

Nakajima, N; Higo, J; Kidera, A; Nakamura, H

2000-02-11

The free energy landscapes of peptide conformations in water have been observed by the enhanced conformational sampling method, applying the selectively enhanced multicanonical molecular dynamics simulations. The conformations of the peptide dimers, -Gly-Gly-, -Gly-Ala-, -Gly-Ser-, -Ala-Gly-, -Asn-Gly-, -Pro-Gly-, -Pro-Ala-, and -Ala-Ala-, which were all blocked with N-terminal acetyl and C-terminal N-methyl groups, were individually sampled with the explicit TIP3P water molecules. From each simulation trajectory, we obtained the canonical ensemble at 300 K, from which the individual three-dimensional landscape was drawn by the potential of mean force using the three reaction coordinates: the backbone dihedral angle, psi, of the first amino acid, the backbone dihedral angle, phi, of the second amino acid, and the distance between the carbonyl oxygen of the N-terminal acetyl group and the C-terminal amide proton. The most stable state and several meta-stable states correspond to extended conformations and typical beta-turn conformations, and their free energy values were accounted for from the potentials of mean force at the states. In addition, the contributions from the intra-molecular energies of peptides and those from the hydration effects were analyzed. Consequently, the stable beta-turn conformations in the free energy landscape were consistent with the empirically preferred beta-turn types for each amino acid sequence. The thermodynamic values for the hydration effect were decomposed and they correlated well with the empirical values estimated from the solvent accessible surface area of each molecular conformation during the trajectories. The origin of the architecture of protein local fragments was analyzed from the viewpoint of the free energy and its decomposed factors. Copyright 2000 Academic Press.

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.

PubMed

Galvelis, Raimondas; Sugita, Yuji

2017-06-13

The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e., importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbor density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation. The bias potential is constructed iteratively from short biased MD simulations accounting for correlation among CVs. Our method is capable of achieving ergodic sampling and calculating free energy of polypeptides with up to 8-dimensional bias potential.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

PubMed

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-07-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms☆

PubMed Central

Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

2016-01-01

This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins. Guest Editors: J.C. Gumbart and Sergei Noskov. PMID:26766517

Enhanced Cleaning of Genesis Solar Wind Sample 61348 for Film Residue Removal

NASA Technical Reports Server (NTRS)

Allums, K. K.; Gonzalez, C. P.; Kuhlman, K. R.; Allton, J. H.

2015-01-01

The Genesis mission returned to Earth on September 8, 2004, experiencing a nonnominal reentry. During the recovery of the collector materials from the capsule, many of the collector fragments were placed on the adhesive protion of post-it notes to prevent the fragments from moving during transport back to Johnson Space Center. This unknowingly provided an additional contaminate that would prove difficult to remove with the limited chemistries allowed in the Genesis Curation Laboratory. Generally when collector material samples are prepared for allocation to PIs, the samples are cleaned front side only with Ultra-Pure Water (UPW) via megasonic dispersion to the collector surface to remove crash debris and contamination. While this cleaning method works well on samples that were not placed on post-its during recovery, it has caused movement of the residue on the back of the sample to be deposited on the front in at least two examples. Therefore, samples placed on the adhesive portion on post-it note, require enhanced cleaning methods since post-it residue has proved resistant to UPW cleaning.

Adaptive enhanced sampling by force-biasing using neural networks

NASA Astrophysics Data System (ADS)

Guo, Ashley Z.; Sevgen, Emre; Sidky, Hythem; Whitmer, Jonathan K.; Hubbell, Jeffrey A.; de Pablo, Juan J.

2018-04-01

A machine learning assisted method is presented for molecular simulation of systems with rugged free energy landscapes. The method is general and can be combined with other advanced sampling techniques. In the particular implementation proposed here, it is illustrated in the context of an adaptive biasing force approach where, rather than relying on discrete force estimates, one can resort to a self-regularizing artificial neural network to generate continuous, estimated generalized forces. By doing so, the proposed approach addresses several shortcomings common to adaptive biasing force and other algorithms. Specifically, the neural network enables (1) smooth estimates of generalized forces in sparsely sampled regions, (2) force estimates in previously unexplored regions, and (3) continuous force estimates with which to bias the simulation, as opposed to biases generated at specific points of a discrete grid. The usefulness of the method is illustrated with three different examples, chosen to highlight the wide range of applicability of the underlying concepts. In all three cases, the new method is found to enhance considerably the underlying traditional adaptive biasing force approach. The method is also found to provide improvements over previous implementations of neural network assisted algorithms.

Enhancing resolution of free-flow zone electrophoresis via a simple sheath-flow sample injection.

PubMed

Yang, Ying; Kong, Fan-Zhi; Liu, Ji; Li, Jun-Min; Liu, Xiao-Ping; Li, Guo-Qing; Wang, Ju-Fang; Xiao, Hua; Fan, Liu-Yin; Cao, Cheng-Xi; Li, Shan

2016-07-01

In this work, a simple and novel sheath-flow sample injection method (SFSIM) is introduced to reduce the band broadening of free-flow zone electrophoresis separation in newly developed self-balance free-flow electrophoresis instrument. A needle injector was placed in the center of the separation inlet, into which the BGE and sample solution were pumped simultaneously. BGE formed sheath flow outside the sample stream, resulting in less band broadening related to hydrodynamics and electrodynamics. Hemoglobin and C-phycocyanin were successfully separated by the proposed method in contrast to the poor separation of free-flow electrophoresis with the traditional injection method without sheath flow. About 3.75 times resolution enhancement could be achieved by sheath-flow sample injection method. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accounting for receptor flexibility and enhanced sampling methods in computer-aided drug design.

PubMed

Sinko, William; Lindert, Steffen; McCammon, J Andrew

2013-01-01

Protein flexibility plays a major role in biomolecular recognition. In many cases, it is not obvious how molecular structure will change upon association with other molecules. In proteins, these changes can be major, with large deviations in overall backbone structure, or they can be more subtle as in a side-chain rotation. Either way the algorithms that predict the favorability of biomolecular association require relatively accurate predictions of the bound structure to give an accurate assessment of the energy involved in association. Here, we review a number of techniques that have been proposed to accommodate receptor flexibility in the simulation of small molecules binding to protein receptors. We investigate modifications to standard rigid receptor docking algorithms and also explore enhanced sampling techniques, and the combination of free energy calculations and enhanced sampling techniques. The understanding and allowance for receptor flexibility are helping to make computer simulations of ligand protein binding more accurate. These developments may help improve the efficiency of drug discovery and development. Efficiency will be essential as we begin to see personalized medicine tailored to individual patients, which means specific drugs are needed for each patient's genetic makeup. © 2012 John Wiley & Sons A/S.

Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods.

PubMed

Abella, Jayvee R; Moll, Mark; Kavraki, Lydia E

2018-01-01

The ability to efficiently sample structurally diverse protein conformations allows one to gain a high-level view of a protein's energy landscape. Algorithms from robot motion planning have been used for conformational sampling, and several of these algorithms promote diversity by keeping track of "coverage" in conformational space based on the local sampling density. However, large proteins present special challenges. In particular, larger systems require running many concurrent instances of these algorithms, but these algorithms can quickly become memory intensive because they typically keep previously sampled conformations in memory to maintain coverage estimates. In addition, robotics-inspired algorithms depend on defining useful perturbation strategies for exploring the conformational space, which is a difficult task for large proteins because such systems are typically more constrained and exhibit complex motions. In this article, we introduce two methodologies for maintaining and enhancing diversity in robotics-inspired conformational sampling. The first method addresses algorithms based on coverage estimates and leverages the use of a low-dimensional projection to define a global coverage grid that maintains coverage across concurrent runs of sampling. The second method is an automatic definition of a perturbation strategy through readily available flexibility information derived from B-factors, secondary structure, and rigidity analysis. Our results show a significant increase in the diversity of the conformations sampled for proteins consisting of up to 500 residues when applied to a specific robotics-inspired algorithm for conformational sampling. The methodologies presented in this article may be vital components for the scalability of robotics-inspired approaches.

Towards high concentration enhancement of microfluidic temperature gradient focusing of sample solutes using combined AC and DC field induced Joule heating.

PubMed

Ge, Zhengwei; Wang, Wei; Yang, Chun

2011-04-07

It is challenging to continuously concentrate sample solutes in microfluidic channels. We present an improved electrokinetic technique for enhancing microfluidic temperature gradient focusing (TGF) of sample solutes using combined AC and DC field induced Joule heating effects. The introduction of an AC electric field component services dual functions: one is to produce Joule heat for generating temperature gradient; the other is to suppress electroosmotic flow. Consequently the required DC voltages for achieving sample concentration by Joule heating induced TGF are reduced, thereby leading to smaller electroosmotic flow (EOF) and thus backpressure effects. As a demonstration, the proposed technique can lead to concentration enhancement of sample solutes of more than 2500-fold, which is much higher than the existing literature reported microfluidic concentration enhancement by utilizing the Joule heating induced TGF technique.

Preserving, Enhancing, and Continuing the Scientific Legacy of the Apollo Sample Suite

NASA Astrophysics Data System (ADS)

Zeigler, R. A.; Evans, C. A.; Lehnert, K.; Cai, Y.; Todd, N. S.

2016-12-01

From 1969 to 1972, Apollo astronauts collected 382 kg of rocks, soils, and core samples from six geologically diverse locations on the Moon. In the nearly 50 years since the samples were collected, over 3000 different studies have been conducted using the nearly 2200 different Apollo samples. Despite the maturity of the sample collection, many new studies of lunar samples are undertaken each year, with an average of >55 requests and >600 distinct subsamples allocated annually over the past five years. The Apollo samples are a finite resource, however. Although new studies are encouraged, it is important that new studies do not duplicate previous studies, and where possible, leverage previous results to inform and enhance the current studies. This helps to preserve the samples and scientific funding, both of which are precious resources. We have initiated several new efforts to rescue some of the early analyses from these samples, including unpublished analytical data. We are actively scanning NASA documentation in paper form that is related to the Apollo missions and sample processing, and we are collaborating with IEDA to establish a geochemical data base called MoonDB. To populate this database, we are actively working with about a dozen prominent lunar PIs to organize and transcribe years of both published and unpublished data, making it available to all researchers. This effort will also take advantage of new online analytical tools like PetDB. There have already been tangible results from the MoonDB data rescue effort. A pilot project involving the rescue of geochemical data of John Delano on Apollo pyroclastic glasses has already been referenced in multiple Apollo sample requests, and in fact, the compiled data was used as part of one of the new studies. Similarly, scanned sample handling reports have been utilized to find previously analyzed samples that were appropriate to fulfill new sample requests. We have also begun to image the Apollo samples using (1

Energy Landscape of All-Atom Protein-Protein Interactions Revealed by Multiscale Enhanced Sampling

PubMed Central

Moritsugu, Kei; Terada, Tohru; Kidera, Akinori

2014-01-01

Protein-protein interactions are regulated by a subtle balance of complicated atomic interactions and solvation at the interface. To understand such an elusive phenomenon, it is necessary to thoroughly survey the large configurational space from the stable complex structure to the dissociated states using the all-atom model in explicit solvent and to delineate the energy landscape of protein-protein interactions. In this study, we carried out a multiscale enhanced sampling (MSES) simulation of the formation of a barnase-barstar complex, which is a protein complex characterized by an extraordinary tight and fast binding, to determine the energy landscape of atomistic protein-protein interactions. The MSES adopts a multicopy and multiscale scheme to enable for the enhanced sampling of the all-atom model of large proteins including explicit solvent. During the 100-ns MSES simulation of the barnase-barstar system, we observed the association-dissociation processes of the atomistic protein complex in solution several times, which contained not only the native complex structure but also fully non-native configurations. The sampled distributions suggest that a large variety of non-native states went downhill to the stable complex structure, like a fast folding on a funnel-like potential. This funnel landscape is attributed to dominant configurations in the early stage of the association process characterized by near-native orientations, which will accelerate the native inter-molecular interactions. These configurations are guided mostly by the shape complementarity between barnase and barstar, and lead to the fast formation of the final complex structure along the downhill energy landscape. PMID:25340714

Enhanced Sampling Methods for the Computation of Conformational Kinetics in Macromolecules

NASA Astrophysics Data System (ADS)

Grazioli, Gianmarc

Calculating the kinetics of conformational changes in macromolecules, such as proteins and nucleic acids, is still very much an open problem in theoretical chemistry and computational biophysics. If it were feasible to run large sets of molecular dynamics trajectories that begin in one configuration and terminate when reaching another configuration of interest, calculating kinetics from molecular dynamics simulations would be simple, but in practice, configuration spaces encompassing all possible configurations for even the simplest of macromolecules are far too vast for such a brute force approach. In fact, many problems related to searches of configuration spaces, such as protein structure prediction, are considered to be NP-hard. Two approaches to addressing this problem are to either develop methods for enhanced sampling of trajectories that confine the search to productive trajectories without loss of temporal information, or coarse-grained methodologies that recast the problem in reduced spaces that can be exhaustively searched. This thesis will begin with a description of work carried out in the vein of the second approach, where a Smoluchowski diffusion equation model was developed that accurately reproduces the rate vs. force relationship observed in the mechano-catalytic disulphide bond cleavage observed in thioredoxin-catalyzed reduction of disulphide bonds. Next, three different novel enhanced sampling methods developed in the vein of the first approach will be described, which can be employed either separately or in conjunction with each other to autonomously define a set of energetically relevant subspaces in configuration space, accelerate trajectories between the interfaces dividing the subspaces while preserving the distribution of unassisted transition times between subspaces, and approximate time correlation functions from the kinetic data collected from the transitions between interfaces.

Series and parallel arc-fault circuit interrupter tests.

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

Johnson, Jay Dean; Fresquez, Armando J.; Gudgel, Bob

2013-07-01

While the 2011 National Electrical Codeª (NEC) only requires series arc-fault protection, some arc-fault circuit interrupter (AFCI) manufacturers are designing products to detect and mitigate both series and parallel arc-faults. Sandia National Laboratories (SNL) has extensively investigated the electrical differences of series and parallel arc-faults and has offered possible classification and mitigation solutions. As part of this effort, Sandia National Laboratories has collaborated with MidNite Solar to create and test a 24-string combiner box with an AFCI which detects, differentiates, and de-energizes series and parallel arc-faults. In the case of the MidNite AFCI prototype, series arc-faults are mitigated by openingmore » the PV strings, whereas parallel arc-faults are mitigated by shorting the array. A range of different experimental series and parallel arc-fault tests with the MidNite combiner box were performed at the Distributed Energy Technologies Laboratory (DETL) at SNL in Albuquerque, NM. In all the tests, the prototype de-energized the arc-faults in the time period required by the arc-fault circuit interrupt testing standard, UL 1699B. The experimental tests confirm series and parallel arc-faults can be successfully mitigated with a combiner box-integrated solution.« less

Glass composition and solution speciation effects on stage III dissolution

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

Trivelpiece, Cory L.; Rice, Jarret A.; Pantano, Carlo G.

To understand and mitigate the onset of Stage III corrosion of multicomponent oxides waste glasses. Stage III refers to a resumption of the high initial rate of glass dissolution in some glass samples that have otherwise exhibited dissolution at the much lower residual rate for a long time (Stage II). Although the onset of Stage III is known to occur concurrently with the precipitation of particular alteration products, the root cause of the transition is still unknown. Certain glass compositions (notably AFCI) and high pH environmental conditions are also associated with this observed transition.

Preserving, Enhancing, and Continuing the Scientific Legacy of the Apollo Sample Suite

NASA Technical Reports Server (NTRS)

Zeigler, Ryan; Evans, Cindy; Cai, Yue; Lehnert, Kerstin; Todd, Nancy; Blumenfeld, Erika

2016-01-01

From 1969 to 1972, Apollo astronauts collected 382 kg of rocks, soils, and core samples from six geologically diverse locations on the Moon. In the nearly 50 years since the samples were collected, over 3000 different studies have been conducted using the nearly 2200 different Apollo samples. Despite the maturity of the sample collection, many new studies of lunar samples are undertaken each year, with an average of more than 55 requests and more than 600 distinct subsamples allocated annually over the past five years. The Apollo samples are a finite resource, however. Although new studies are encouraged, it is important that new studies do not duplicate previous studies, and where possible, leverage previous results to inform and enhance the current studies. This helps to preserve the samples and scientific funding, both of which are precious resources. We have initiated several new efforts to rescue some of the early analyses from these samples, including unpublished analytical data. We are actively scanning NASA documentation in paper form that is related to the Apollo missions and sample processing, and we are collaborating with IEDA to establish a geochemical data base called MoonDB. To populate this database, we are actively working with about a dozen prominent lunar PIs to organize and transcribe years of both published and unpublished data, making it available to all researchers. This effort will also take advantage of new online analytical tools like PetDB. There have already been tangible results from the MoonDB data rescue effort. A pilot project involving the rescue of geochemical data of John Delano on Apollo pyroclastic glasses has already been referenced in multiple Apollo sample requests, and in fact, the compiled data was used as part of one of the new studies. Similarly, scanned sample handling reports have been utilized to find previously analyzed samples that were appropriate to fulfill new sample requests. We have also begun to image the Apollo

Water-soluble cyclodextrin polymers for enhanced relative recovery of hydrophobic analytes during microdialysis sampling.

PubMed

Ao, Xiaoping; Stenken, Julie A

2003-09-01

Microdialysis relative recovery (RR) enhancement using different water-soluble, epichlorohydrin-based cyclodextrin polymers (CD-EPS) was studied in vitro for different analytes, amitryptiline, carbamazepine, hydroquinone, ibuprofen, and 4-nitrophenol. When compared to the native CDs (alpha, beta, and gamma) on a per mole basis, the CD-EPS enhanced microdialysis RR was either statistically greater or the same. beta-CD-EPS was more highly retained than native beta-CD by a 20 000 Da molecular weight cutoff (MWCO) polycarbonate membrane, but showed no statistical difference for loss across a 100 000 Da MWCO polyethersulfone membrane (PES). When the same weight percent of beta-CD or beta-CD-EPS was included in the microdialysis perfusion fluid, the beta-CD-EPS produced a higher microdialysis RR than native beta-CD for all analytes across the PES membrane. However, enhancements for the PC membrane were statistically insignificant when beta-CD and beta-CD-EPS were compared on a per mole basis. These results suggest that CD-EPS may be used as effective enhancement agents during microdialysis sampling and for some membranes provide the additional advantage of being retained more than native CDs.

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.

Latin Hypercube Sampling (LHS) at variable resolutions for enhanced watershed scale Soil Sampling and Digital Soil Mapping.

NASA Astrophysics Data System (ADS)

Hamalainen, Sampsa; Geng, Xiaoyuan; He, Juanxia

2017-04-01

Latin Hypercube Sampling (LHS) at variable resolutions for enhanced watershed scale Soil Sampling and Digital Soil Mapping. Sampsa Hamalainen, Xiaoyuan Geng, and Juanxia, He. AAFC - Agriculture and Agr-Food Canada, Ottawa, Canada. The Latin Hypercube Sampling (LHS) approach to assist with Digital Soil Mapping has been developed for some time now, however the purpose of this work was to complement LHS with use of multiple spatial resolutions of covariate datasets and variability in the range of sampling points produced. This allowed for specific sets of LHS points to be produced to fulfil the needs of various partners from multiple projects working in the Ontario and Prince Edward Island provinces of Canada. Secondary soil and environmental attributes are critical inputs that are required in the development of sampling points by LHS. These include a required Digital Elevation Model (DEM) and subsequent covariate datasets produced as a result of a Digital Terrain Analysis performed on the DEM. These additional covariates often include but are not limited to Topographic Wetness Index (TWI), Length-Slope (LS) Factor, and Slope which are continuous data. The range of specific points created in LHS included 50 - 200 depending on the size of the watershed and more importantly the number of soil types found within. The spatial resolution of covariates included within the work ranged from 5 - 30 m. The iterations within the LHS sampling were run at an optimal level so the LHS model provided a good spatial representation of the environmental attributes within the watershed. Also, additional covariates were included in the Latin Hypercube Sampling approach which is categorical in nature such as external Surficial Geology data. Some initial results of the work include using a 1000 iteration variable within the LHS model. 1000 iterations was consistently a reasonable value used to produce sampling points that provided a good spatial representation of the environmental

An enhanced droplet-based liquid microjunction surface sampling system coupled with HPLC-ESI-MS/MS for spatially resolved analysis

DOE PAGES

Van Berkel, Gary J.; Weiskittel, Taylor M.; Kertesz, Vilmos

2014-11-07

Droplet-based liquid microjunction surface sampling coupled with high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) for spatially resolved analysis provides the possibility of effective analysis of complex matrix samples and can provide a greater degree of chemical information from a single spot sample than is typically possible with a direct analysis of an extract. Described here is the setup and enhanced capabilities of a discrete droplet liquid microjunction surface sampling system employing a commercially available CTC PAL autosampler. The system enhancements include incorporation of a laser distance sensor enabling unattended analysis of samples and sample locations of dramatically disparatemore » height as well as reliably dispensing just 0.5 μL of extraction solvent to make the liquid junction to the surface, wherein the extraction spot size was confined to an area about 0.7 mm in diameter; software modifications improving the spatial resolution of sampling spot selection from 1.0 to 0.1 mm; use of an open bed tray system to accommodate samples as large as whole-body rat thin tissue sections; and custom sample/solvent holders that shorten sampling time to approximately 1 min per sample. Lastly, the merit of these new features was demonstrated by spatially resolved sampling, HPLC separation, and mass spectral detection of pharmaceuticals and metabolites from whole-body rat thin tissue sections and razor blade (“crude”) cut mouse tissue.« less

An enhanced droplet-based liquid microjunction surface sampling system coupled with HPLC-ESI-MS/MS for spatially resolved analysis

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

Van Berkel, Gary J.; Weiskittel, Taylor M.; Kertesz, Vilmos

Droplet-based liquid microjunction surface sampling coupled with high-performance liquid chromatography (HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) for spatially resolved analysis provides the possibility of effective analysis of complex matrix samples and can provide a greater degree of chemical information from a single spot sample than is typically possible with a direct analysis of an extract. Described here is the setup and enhanced capabilities of a discrete droplet liquid microjunction surface sampling system employing a commercially available CTC PAL autosampler. The system enhancements include incorporation of a laser distance sensor enabling unattended analysis of samples and sample locations of dramatically disparatemore » height as well as reliably dispensing just 0.5 μL of extraction solvent to make the liquid junction to the surface, wherein the extraction spot size was confined to an area about 0.7 mm in diameter; software modifications improving the spatial resolution of sampling spot selection from 1.0 to 0.1 mm; use of an open bed tray system to accommodate samples as large as whole-body rat thin tissue sections; and custom sample/solvent holders that shorten sampling time to approximately 1 min per sample. Lastly, the merit of these new features was demonstrated by spatially resolved sampling, HPLC separation, and mass spectral detection of pharmaceuticals and metabolites from whole-body rat thin tissue sections and razor blade (“crude”) cut mouse tissue.« less

Determination of finasteride and its metabolite in urine by dispersive liquid-liquid microextraction combined with field-enhanced sample stacking and sweeping.

PubMed

Chen, Chun-Hsien; Chao, Yu-Ying; Lin, Yi-Hui; Chen, Yen-Ling

2018-04-27

The on-line preconcentration technique of field-enhanced sample stacking and sweeping (FESS-sweeping) are combined with dispersive liquid-liquid microextraction (DLLME) to monitor the concentrations of finasteride, which is used in the treatment of androgenetic alopecia, and its metabolite, finasteride carboxylic acid (M3), in urine samples. DLLME is used to concentrate and eliminate the interferences of urine samples and uses chloroform as an extracting solvent and acetonitrile as a disperser solvent. A high conductivity buffer (HCB) was introduced into capillary and then sample plug (90.7% capillary length) was injected into capillary. After applying voltage, the sodium dodecyl sulfate (SDS) swept the analytes from the low conductivity sample solution into HCB. The analytes were concentrated on the field-enhanced sample stacking boundary. The limit of detection for the analytes is 20 ng mL -1 . The sensitivity enrichment of finasteride and M3 are 362-fold and 480-fold, respectively, compared with the conventional MEKC method. The on-line preconcentration technique of field-enhanced sample stacking and sweeping possess good selectivity because the endogenous steroid did not interfere the detection of finasteride and M3. The analytical technique is applied to investigate the concentrations in urine samples from patients who have been administered finasteride for the treatment of androgenetic alopecia; the amount of M3 detected in 12 h was 72.69 ± 4.18 μg. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

NASA Astrophysics Data System (ADS)

Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

2018-01-01

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

PubMed

Suh, Donghyuk; Radak, Brian K; Chipot, Christophe; Roux, Benoît

2018-01-07

Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

Electro-enhanced hollow fiber membrane liquid phase microextraction of Cr(VI) oxoanions in drinking water samples.

PubMed

Chanthasakda, Nattaporn; Nitiyanontakit, Sira; Varanusupakul, Pakorn

2016-02-01

Hollow fiber membrane liquid phase microextraction (HF-LPME) of metal oxoanions was studied using an ionic carrier enhanced by the application of an electric field (electro-enhanced HF-LPME). The Cr(VI) oxoanion was used as the model. The transportation of Cr(VI) oxoanions across the supported liquid membrane (SLM) was explored via the ion-exchange process and electrokinetic migration. The type of SLM, type of acceptor solution, extraction time, electric potential, and stirring rate were investigated and optimized using MilliQ water. Electro-enhanced HF-LPME provided a much higher enrichment factor compared to conventional HF-LPME (no electric potential) for the same extraction time. A mixture of an anion exchange carrier (methyltrialkyl-ammonium chloride, Aliquat 336) in the SLM facilitated the transportation of Cr(VI) oxoanions. The SLM that gave the best performance was 1-heptanol mixed with 5% Aliquat 336 with 1M NaOH as the acceptor. Linearity was obtained in the working range of 3-15 µg L(-1) Cr(VI) (R(2)>0.99) at 30 V with a 5 min extraction time. The limit of detection was below 5 µg L(-1). The relative standard deviation was less than 12%. The method was applied to drinking water samples. The recoveries of spiked Cr(VI) in drinking water samples were in the range of 96-101% based on the matrix-matched calibration curves. The method was limited to samples containing low levels of ions due to the occurrence of electrolysis. The type of SLM, particularly regarding its resistance, should be tuned to control this problematic phenomenon. Copyright © 2015 Elsevier B.V. All rights reserved.

A Review of Enhanced Sampling Approaches for Accelerated Molecular Dynamics

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush; van de Walle, Axel

Molecular dynamics (MD) simulations have become a tool of immense use and popularity for simulating a variety of systems. With the advent of massively parallel computer resources, one now routinely sees applications of MD to systems as large as hundreds of thousands to even several million atoms, which is almost the size of most nanomaterials. However, it is not yet possible to reach laboratory timescales of milliseconds and beyond with MD simulations. Due to the essentially sequential nature of time, parallel computers have been of limited use in solving this so-called timescale problem. Instead, over the years a large range of statistical mechanics based enhanced sampling approaches have been proposed for accelerating molecular dynamics, and accessing timescales that are well beyond the reach of the fastest computers. In this review we provide an overview of these approaches, including the underlying theory, typical applications, and publicly available software resources to implement them.

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations.

PubMed

Oleinikovas, Vladimiras; Saladino, Giorgio; Cossins, Benjamin P; Gervasio, Francesco L

2016-11-02

Cryptic pockets, that is, sites on protein targets that only become apparent when drugs bind, provide a promising alternative to classical binding sites for drug development. Here, we investigate the nature and dynamical properties of cryptic sites in four pharmacologically relevant targets, while comparing the efficacy of various simulation-based approaches in discovering them. We find that the studied cryptic sites do not correspond to local minima in the computed conformational free energy landscape of the unliganded proteins. They thus promptly close in all of the molecular dynamics simulations performed, irrespective of the force-field used. Temperature-based enhanced sampling approaches, such as Parallel Tempering, do not improve the situation, as the entropic term does not help in the opening of the sites. The use of fragment probes helps, as in long simulations occasionally it leads to the opening and binding to the cryptic sites. Our observed mechanism of cryptic site formation is suggestive of an interplay between two classical mechanisms: induced-fit and conformational selection. Employing this insight, we developed a novel Hamiltonian Replica Exchange-based method "SWISH" (Sampling Water Interfaces through Scaled Hamiltonians), which combined with probes resulted in a promising general approach for cryptic site discovery. We also addressed the issue of "false-positives" and propose a simple approach to distinguish them from druggable cryptic pockets. Our simulations, whose cumulative sampling time was more than 200 μs, help in clarifying the molecular mechanism of pocket formation, providing a solid basis for the choice of an efficient computational method.

Enhanced aerodynamic reach of vapor and aerosol sampling for real-time mass spectrometric detection using Venturi-assisted entrainment and ionization

PubMed Central

Forbes, Thomas P.; Staymates, Matthew

2017-01-01

Venturi-assisted ENTrainment and Ionization (VENTI) was developed, demonstrating efficient entrainment, collection, and transport of remotely sampled vapors, aerosols, and dust particulate for real-time mass spectrometry (MS) detection. Integrating the Venturi and Coandă effects at multiple locations generated flow and analyte transport from non-proximate locations and more importantly enhanced the aerodynamic reach at the point of collection. Transport through remote sampling probes up to 2.5 m in length was achieved with residence times on the order of 10-2 s to 10-1 s and Reynolds numbers on the order of 103 to 104. The Venturi-assisted entrainment successfully enhanced vapor collection and detection by greater than an order of magnitude at 20 cm stand-off (limit of simple suction). This enhancement is imperative, as simple suction restricts sampling to the immediate vicinity, requiring close proximity to the vapor source. In addition, the overall aerodynamic reach distance was increased by approximately 3-fold over simple suction under the investigated conditions. Enhanced aerodynamic reach was corroborated and observed with laser-light sheet flow visualization and schlieren imaging. Coupled with atmospheric pressure chemical ionization (APCI), the detection of a range of volatile chemical vapors; explosive vapors; explosive, narcotic, and mustard gas surrogate (methyl salicylate) aerosols; and explosive dust particulate was demonstrated. Continuous real-time Venturi-assisted monitoring of a large room (approximately 90 m2 area, 570 m3 volume) was demonstrated for a 60-minute period without the remote sampling probe, exhibiting detection of chemical vapors and methyl salicylate at approximately 3 m stand-off distances within 2 minutes of exposure. PMID:28107830

Enhanced aerodynamic reach of vapor and aerosol sampling for real-time mass spectrometric detection using Venturi-assisted entrainment and ionization.

PubMed

Forbes, Thomas P; Staymates, Matthew

2017-03-08

Venturi-assisted ENTrainment and Ionization (VENTI) was developed, demonstrating efficient entrainment, collection, and transport of remotely sampled vapors, aerosols, and dust particulate for real-time mass spectrometry (MS) detection. Integrating the Venturi and Coandă effects at multiple locations generated flow and analyte transport from non-proximate locations and more importantly enhanced the aerodynamic reach at the point of collection. Transport through remote sampling probes up to 2.5 m in length was achieved with residence times on the order of 10 -2  s to 10 -1  s and Reynolds numbers on the order of 10 3 to 10 4 . The Venturi-assisted entrainment successfully enhanced vapor collection and detection by greater than an order of magnitude at 20 cm stand-off (limit of simple suction). This enhancement is imperative, as simple suction restricts sampling to the immediate vicinity, requiring close proximity to the vapor source. In addition, the overall aerodynamic reach distance was increased by approximately 3-fold over simple suction under the investigated conditions. Enhanced aerodynamic reach was corroborated and observed with laser-light sheet flow visualization and schlieren imaging. Coupled with atmospheric pressure chemical ionization (APCI), the detection of a range of volatile chemical vapors; explosive vapors; explosive, narcotic, and mustard gas surrogate (methyl salicylate) aerosols; and explosive dust particulate was demonstrated. Continuous real-time Venturi-assisted monitoring of a large room (approximately 90 m 2 area, 570 m 3 volume) was demonstrated for a 60-min period without the remote sampling probe, exhibiting detection of chemical vapors and methyl salicylate at approximately 3 m stand-off distances within 2 min of exposure. Published by Elsevier B.V.

Resolution-enhancement and sampling error correction based on molecular absorption line in frequency scanning interferometry

NASA Astrophysics Data System (ADS)

Pan, Hao; Qu, Xinghua; Shi, Chunzhao; Zhang, Fumin; Li, Yating

2018-06-01

The non-uniform interval resampling method has been widely used in frequency modulated continuous wave (FMCW) laser ranging. In the large-bandwidth and long-distance measurements, the range peak is deteriorated due to the fiber dispersion mismatch. In this study, we analyze the frequency-sampling error caused by the mismatch and measure it using the spectroscopy of molecular frequency references line. By using the adjacent points' replacement and spline interpolation technique, the sampling errors could be eliminated. The results demonstrated that proposed method is suitable for resolution-enhancement and high-precision measurement. Moreover, using the proposed method, we achieved the precision of absolute distance less than 45 μm within 8 m.

Detection of tobacco-related biomarkers in urine samples by surface-enhanced Raman spectroscopy coupled with thin-layer chromatography.

PubMed

Huang, Rongfu; Han, Sungyub; Li, Xiao Sheryl

2013-08-01

The nicotine metabolites, cotinine and trans-3'-hydroxycotinine (3HC) are considered as superior biomarkers for identifying tobacco exposure. More importantly, the ratio of 3HC to cotinine is a good indicator to phenotype individuals for cytochrome P450 2A6 activity and to individualize pharmacotherapy for tobacco addiction. In this paper, a simple, robust and novel method based on surface-enhanced Raman spectroscopy coupled with thin-layer chromatography (TLC) was developed to directly quantify the biomarkers in human urine samples. This is the first time surface-enhanced Raman spectroscopy (SERS) was used to detect cotinine and 3HC in urine samples. The linear dynamic range for the detection of cotinine is from 40 nM to 8 μM while that of 3HC is from 1 μM to 15 μM. The detection limits are 10 nM and 0.2 μM for cotinine and 3HC, respectively. The proposed method was further validated by quantifying the concentration of both cotinine and 3HC in smokers' urine samples. This TLC-SERS method allows the direct detection of cotinine in the urine samples of both active and passive smokers and the detection of 3HC in smokers.

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

Silver Nanoparticle-Enhanced Resonance Raman Sensor of Chromium(III) in Seawater Samples.

PubMed

Ly, Nguyễn Hoàng; Joo, Sang-Woo

2015-04-29

Tris(hydroxymethyl)aminomethane ethylenediaminetetraacetic acid (Tris-EDTA), upon binding Cr(III) in aqueous solutions at pH 8.0 on silver nanoparticles (AgNPs), was found to provide a sensitive and selective Raman marker band at ~563 cm-1, which can be ascribed to the metal-N band. UV-Vis absorption spectra also supported the aggregation and structural change of EDTA upon binding Cr(III). Only for Cr(III) concentrations above 500 nM, the band at ~563 cm-1 become strongly intensified in the surface-enhanced Raman scattering spectra. This band, due to the metal-EDTA complex, was not observed in the case of 50 mM of K+, Cd2+, Mg2+, Ca2+, Mn2+, Co2+, Na+, Cu2+, NH4+, Hg2+, Ni2+, Fe3+, Pb2+, Fe2+, and Zn2+ ions. Seawater samples containing K, Mg, Ca, and Na ion concentrations higher than 8 mM also showed the characteristic Raman band at ~563 cm-1 above 500 nM, validating our method. Our approach may be useful in detecting real water samples by means of AgNPs and Raman spectroscopy.

Comparison of field-enhanced and pressure-assisted field-enhanced sample injection techniques for the analysis of water-soluble vitamins using CZE.

PubMed

Liu, Qingqing; Liu, Yaling; Guan, Yu; Jia, Li

2009-04-01

A new online concentration method, namely pressure-assisted field-enhanced sample injection (PA-FESI), was developed and compared with FESI for the analysis of water-soluble vitamins by CZE with UV detection. In PA-FESI, negative voltage and positive pressure were simultaneously applied to initialize PA-FESI. PA-FESI uses the hydrodynamic flow generated by the positive pressure to counterbalance the reverse EOF in the capillary column during electrokinetic sample injection, which allowed a longer injection time than usual FESI mode without compromising the separation efficiency. Using the PA-FESI method, the LODs of the vitamins were at ng/mL level based on the S/N of 3 and the RSDs of migration time and peak area for each vitamin (1 microg/mL) were less than 5.1%. The developed method was applied to the analysis of water-soluble vitamins in corns.

Exploiting LBL-assembled Au nanoparticles to enhance Raman signals for point-of-care testing of osteoporosis with excreta sample

NASA Astrophysics Data System (ADS)

Sun, Jian F.; Liu, Xuan; Guo, Zhi R.; Dong, Jian; Huang, Yawen; Zhang, Jie; Jin, Hui; Gu, Ning

2017-02-01

Due to the intrinsic lack of specific biomarkers, there is an increasing demand for degenerative diseases to develop a testing method independent upon the targeting biomolecules. In this paper, we proposed a novel idea for this issue which was to analyze the characteristic information of metabolites with Raman spectrum. First, we achieved the fabrication of stable, uniform and reproducible substrate to enhance the Raman signals, which is crucial to the following analysis of information. This idea was confirmed with the osteoporosis-modeled mice. Furthermore, the testing results with clinical samples also preliminarily exhibited the feasibility of this strategy. The substrate to enhance Raman signal was fabricated by the layer-by-layer assembly of Au nanoparticles. The osteoporosis modeling was made by bilateral ovariectomy. Ten female mice were randomly divided into two groups. The urine and dejecta samples of mice were collected every week. Clinic urine samples were collected from patients with osteoporosis while the controlled samples were from the young students in our university. The LBL-assembled substrate of Au nanoparticles was uniform, stable and reproducible to significantly enhance the Raman signals from tiny amount of samples. With a simple data processing technique, the Raman signal-based method can effectively reflect the development of osteoporosis by comparison with micro-CT characterization. Moreover, the Raman signal from samples of clinic patients also showed the obvious difference with that of the control. Raman spectrum may be a good tool to convey the pathological information of metabolites in molecular level. Our results manifested that the information-based testing is possibly feasible and promising. Our strategy utilizes the characteristic information rather than the biological recognition to test the diseases which are difficult to find specific biomarkers. This will be greatly beneficial to the prevention and diagnosis of degenerative

Identification of Metal Oxide Nanoparticles in Histological Samples by Enhanced Darkfield Microscopy and Hyperspectral Mapping.

PubMed

Roth, Gary A; Sosa Peña, Maria del Pilar; Neu-Baker, Nicole M; Tahiliani, Sahil; Brenner, Sara A

2015-12-08

Nanomaterials are increasingly prevalent throughout industry, manufacturing, and biomedical research. The need for tools and techniques that aid in the identification, localization, and characterization of nanoscale materials in biological samples is on the rise. Currently available methods, such as electron microscopy, tend to be resource-intensive, making their use prohibitive for much of the research community. Enhanced darkfield microscopy complemented with a hyperspectral imaging system may provide a solution to this bottleneck by enabling rapid and less expensive characterization of nanoparticles in histological samples. This method allows for high-contrast nanoscale imaging as well as nanomaterial identification. For this technique, histological tissue samples are prepared as they would be for light-based microscopy. First, positive control samples are analyzed to generate the reference spectra that will enable the detection of a material of interest in the sample. Negative controls without the material of interest are also analyzed in order to improve specificity (reduce false positives). Samples can then be imaged and analyzed using methods and software for hyperspectral microscopy or matched against these reference spectra in order to provide maps of the location of materials of interest in a sample. The technique is particularly well-suited for materials with highly unique reflectance spectra, such as noble metals, but is also applicable to other materials, such as semi-metallic oxides. This technique provides information that is difficult to acquire from histological samples without the use of electron microscopy techniques, which may provide higher sensitivity and resolution, but are vastly more resource-intensive and time-consuming than light microscopy.

Nanoparticle-Enhanced Laser Induced Breakdown Spectroscopy for the noninvasive analysis of transparent samples and gemstones.

PubMed

Koral, C; Dell'Aglio, M; Gaudiuso, R; Alrifai, R; Torelli, M; De Giacomo, A

2018-05-15

In this paper, Nanoparticle-Enhanced Laser Induced Breakdown Spectroscopy is applied to transparent samples and gemstones with the aim to overcome the laser induced damage on the sample. We propose to deposit a layer of AuNPs on the sample surface by drying a colloidal solution before ablating the sample with a 532 nm pulsed laser beam. This procedure ensures that the most significant fraction of the beam, being in resonance with the AuNP surface plasmon, is mainly absorbed by the NP layer, which in turn results the breakdown to be induced on NPs rather than on the sample itself. The fast explosion of the NPs and the plasma induction allow the ablation and the transfer in the plasma phase of the portion of sample surface where the NPs were placed. The employed AuNPs are prepared in milliQ water without the use of any chemical stabilizers by Pulsed Laser Ablation in Liquids (PLAL), in order to obtain a strict control of composition and impurities, and to limit possible spectral interferences (except from Au emission lines). Therefore with this technique it is possible to obtain, together with the emission signal of Au (coming from atomized NPs), the emission spectrum of the sample, by limiting or avoiding the direct interaction of the laser pulse with the sample itself. This approach is extremely useful for the elemental analysis by laser ablation of high refractive index samples, where the laser pulse on an untreated surface can otherwise penetrate inside the sample, generate breakdown events below the superficial layer, and consequently cause cracks and other damage. The results obtained with NELIBS on high refractive index samples like glasses, tourmaline, aquamarine and ruby are very promising, and demonstrate the potentiality of this approach for precious gemstones analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

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.

Enhancing sampling design in mist-net bat surveys by accounting for sample size optimization.

PubMed

Trevelin, Leonardo Carreira; Novaes, Roberto Leonan Morim; Colas-Rosas, Paul François; Benathar, Thayse Cristhina Melo; Peres, Carlos A

2017-01-01

The advantages of mist-netting, the main technique used in Neotropical bat community studies to date, include logistical implementation, standardization and sampling representativeness. Nonetheless, study designs still have to deal with issues of detectability related to how different species behave and use the environment. Yet there is considerable sampling heterogeneity across available studies in the literature. Here, we approach the problem of sample size optimization. We evaluated the common sense hypothesis that the first six hours comprise the period of peak night activity for several species, thereby resulting in a representative sample for the whole night. To this end, we combined re-sampling techniques, species accumulation curves, threshold analysis, and community concordance of species compositional data, and applied them to datasets of three different Neotropical biomes (Amazonia, Atlantic Forest and Cerrado). We show that the strategy of restricting sampling to only six hours of the night frequently results in incomplete sampling representation of the entire bat community investigated. From a quantitative standpoint, results corroborated the existence of a major Sample Area effect in all datasets, although for the Amazonia dataset the six-hour strategy was significantly less species-rich after extrapolation, and for the Cerrado dataset it was more efficient. From the qualitative standpoint, however, results demonstrated that, for all three datasets, the identity of species that are effectively sampled will be inherently impacted by choices of sub-sampling schedule. We also propose an alternative six-hour sampling strategy (at the beginning and the end of a sample night) which performed better when resampling Amazonian and Atlantic Forest datasets on bat assemblages. Given the observed magnitude of our results, we propose that sample representativeness has to be carefully weighed against study objectives, and recommend that the trade-off between

Enhancing sampling design in mist-net bat surveys by accounting for sample size optimization

PubMed Central

Trevelin, Leonardo Carreira; Novaes, Roberto Leonan Morim; Colas-Rosas, Paul François; Benathar, Thayse Cristhina Melo; Peres, Carlos A.

2017-01-01

The advantages of mist-netting, the main technique used in Neotropical bat community studies to date, include logistical implementation, standardization and sampling representativeness. Nonetheless, study designs still have to deal with issues of detectability related to how different species behave and use the environment. Yet there is considerable sampling heterogeneity across available studies in the literature. Here, we approach the problem of sample size optimization. We evaluated the common sense hypothesis that the first six hours comprise the period of peak night activity for several species, thereby resulting in a representative sample for the whole night. To this end, we combined re-sampling techniques, species accumulation curves, threshold analysis, and community concordance of species compositional data, and applied them to datasets of three different Neotropical biomes (Amazonia, Atlantic Forest and Cerrado). We show that the strategy of restricting sampling to only six hours of the night frequently results in incomplete sampling representation of the entire bat community investigated. From a quantitative standpoint, results corroborated the existence of a major Sample Area effect in all datasets, although for the Amazonia dataset the six-hour strategy was significantly less species-rich after extrapolation, and for the Cerrado dataset it was more efficient. From the qualitative standpoint, however, results demonstrated that, for all three datasets, the identity of species that are effectively sampled will be inherently impacted by choices of sub-sampling schedule. We also propose an alternative six-hour sampling strategy (at the beginning and the end of a sample night) which performed better when resampling Amazonian and Atlantic Forest datasets on bat assemblages. Given the observed magnitude of our results, we propose that sample representativeness has to be carefully weighed against study objectives, and recommend that the trade-off between

Enhanced conformational sampling via novel variable transformations and very large time-step molecular dynamics

NASA Astrophysics Data System (ADS)

Tuckerman, Mark

2006-03-01

One of the computational grand challenge problems is to develop methodology capable of sampling conformational equilibria in systems with rough energy landscapes. If met, many important problems, most notably protein folding, could be significantly impacted. In this talk, two new approaches for addressing this problem will be presented. First, it will be shown how molecular dynamics can be combined with a novel variable transformation designed to warp configuration space in such a way that barriers are reduced and attractive basins stretched. This method rigorously preserves equilibrium properties while leading to very large enhancements in sampling efficiency. Extensions of this approach to the calculation/exploration of free energy surfaces will be discussed. Next, a new very large time-step molecular dynamics method will be introduced that overcomes the resonances which plague many molecular dynamics algorithms. The performance of the methods is demonstrated on a variety of systems including liquid water, long polymer chains simple protein models, and oligopeptides.

Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

PubMed

Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

2016-12-13

In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate. In this paper, we build on that work and demonstrate that we can calculate high-dimensional free energy surfaces of very high accuracy by incorporating additional terms. The additional terms apply to a set of collective variables which are more coarse than the base set of collective variables. In this way, it is possible to build hierarchical free energy surfaces, which are composed of terms that act on different length scales. We test the accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing simple coarse-grained models and comparing results from the coarse-grained model to results from atomistic simulations. The approach described in this paper is ideally suited for problems in which the free energy surface has important features on different length scales or in which there is some natural hierarchy.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Peter, Emanuel K.

2017-12-01

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation.

PubMed

Peter, Emanuel K

2017-12-07

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Bulk- and surface-modified combinable PDMS capillary sensor array as an easy-to-use sensing device with enhanced sensitivity to elevated concentrations of multiple serum sample components.

PubMed

Fujii, Yuji; Henares, Terence G; Kawamura, Kunio; Endo, Tatsuro; Hisamoto, Hideaki

2012-04-21

To enhance sensitivity and facilitate easy sample introduction into a combinable poly(dimethylsiloxane) (PDMS) capillary (CPC) sensor array, PDMS was modified in bulk and on its surface to prepare "black" PDMS coated with a silver layer and self-assembled monolayer (SAM). India ink, a traditional Japanese black ink, was added to the PDMS pre-polymer for bulk modification. The surface was modified by a silver mirror reaction followed by SAM formation using cysteine. These modifications enhanced the fluorescence signals by reflecting them from the surface and reducing background interference. A decrease in the water contact angle led to enhanced sensitivity and easy sample introduction. Furthermore, a CPC sensor array for multiplex detection of serum sample components was prepared that could quantify the analytes glucose, potassium, and alkaline phosphatase (ALP). When serum samples were introduced by capillary action, the CPC sensor array showed fluorescence responses for each analyte and successfully identified the components with elevated concentrations in the serum samples.

A new class of enhanced kinetic sampling methods for building Markov state models

NASA Astrophysics Data System (ADS)

Bhoutekar, Arti; Ghosh, Susmita; Bhattacharya, Swati; Chatterjee, Abhijit

2017-10-01

Markov state models (MSMs) and other related kinetic network models are frequently used to study the long-timescale dynamical behavior of biomolecular and materials systems. MSMs are often constructed bottom-up using brute-force molecular dynamics (MD) simulations when the model contains a large number of states and kinetic pathways that are not known a priori. However, the resulting network generally encompasses only parts of the configurational space, and regardless of any additional MD performed, several states and pathways will still remain missing. This implies that the duration for which the MSM can faithfully capture the true dynamics, which we term as the validity time for the MSM, is always finite and unfortunately much shorter than the MD time invested to construct the model. A general framework that relates the kinetic uncertainty in the model to the validity time, missing states and pathways, network topology, and statistical sampling is presented. Performing additional calculations for frequently-sampled states/pathways may not alter the MSM validity time. A new class of enhanced kinetic sampling techniques is introduced that aims at targeting rare states/pathways that contribute most to the uncertainty so that the validity time is boosted in an effective manner. Examples including straightforward 1D energy landscapes, lattice models, and biomolecular systems are provided to illustrate the application of the method. Developments presented here will be of interest to the kinetic Monte Carlo community as well.

Mimicking coarse-grained simulations without coarse-graining: enhanced sampling by damping short-range interactions.

PubMed

Wei, Dongshan; Wang, Feng

2010-08-28

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Mimicking coarse-grained simulations without coarse-graining: Enhanced sampling by damping short-range interactions

NASA Astrophysics Data System (ADS)

Wei, Dongshan; Wang, Feng

2010-08-01

The damped-short-range-interaction (DSRI) method is proposed to mimic coarse-grained simulations by propagating an atomistic scale system on a smoothed potential energy surface. The DSRI method has the benefit of enhanced sampling provided by a typical coarse-grained simulation without the need to perform coarse-graining. Our method was used to simulate liquid water, alanine dipeptide folding, and the self-assembly of dimyristoylphosphatidylcholine lipid. In each case, our method appreciably accelerated the dynamics without significantly changing the free energy surface. Additional insights from DSRI simulations and the promise of coupling our DSRI method with Hamiltonian replica-exchange molecular dynamics are discussed.

Surfactant-enhanced spectrofluorimetric determination of total aflatoxins from wheat samples after magnetic solid-phase extraction using modified Fe3O4 nanoparticles

NASA Astrophysics Data System (ADS)

Manafi, Mohammad Hanif; Allahyari, Mehdi; Pourghazi, Kamyar; Amoli-Diva, Mitra; Taherimaslak, Zohreh

2015-07-01

The extraction and preconcentration of total aflatoxins (including aflatoxin B1, B2, G1, and G2) using magnetic nanoparticles based solid phase extraction (MSPE) followed by surfactant-enhanced spectrofluorimetric detection was proposed. Ethylene glycol bis-mercaptoacetate modified silica coated Fe3O4 nanoparticles as an efficient antibody-free adsorbent was successfully applied to extract aflatoxins from wheat samples. High surface area and strong magnetization properties of magnetic nanoparticles were utilized to achieve high enrichment factor (97), and satisfactory recoveries (92-105%) using only 100 mg of the adsorbent. Furthermore, the fast separation time (less than 10 min) avoids many time-consuming cartridge loading or column-passing procedures accompany with the conventional SPE. In determination step, signal enhancement was performed by formation of Triton X-100 micelles around the analytes in 15% (v/v) acetonitrile-water which dramatically increase the sensitivity of the method. Main factors affecting the extraction efficiency and signal enhancement of the analytes including pH of sample solution, desorption conditions, extraction time, sample volume, adsorbent amount, surfactant concentration and volume and time of micelle formation were evaluated and optimized. Under the optimum conditions, wide linear range of 0.1-50 ng mL-1 with low detection limit of 0.03 ng mL-1 were obtained. The developed method was successfully applied to the extraction and preconcentration of aflatoxins in three commercially available wheat samples and the results were compared with the official AOAC method.

Novel Electrosorption-Enhanced Solid-Phase Microextraction Device for Ultrafast In Vivo Sampling of Ionized Pharmaceuticals in Fish.

PubMed

Qiu, Junlang; Wang, Fuxin; Zhang, Tianlang; Chen, Le; Liu, Yuan; Zhu, Fang; Ouyang, Gangfeng

2018-01-02

Decreasing the tedious sample preparation duration is one of the most important concerns for the environmental analytical chemistry especially for in vivo experiments. However, due to the slow mass diffusion paths for most of the conventional methods, ultrafast in vivo sampling remains challenging. Herein, for the first time, we report an ultrafast in vivo solid-phase microextraction (SPME) device based on electrosorption enhancement and a novel custom-made CNT@PPY@pNE fiber for in vivo sampling of ionized acidic pharmaceuticals in fish. This sampling device exhibited an excellent robustness, reproducibility, matrix effect-resistant capacity, and quantitative ability. Importantly, the extraction kinetics of the targeted ionized pharmaceuticals were significantly accelerated using the device, which significantly improved the sensitivity of the SPME in vivo sampling method (limits of detection ranged from 0.12 ng·g -1 to 0.25 ng·g -1 ) and shorten the sampling time (only 1 min). The proposed approach was successfully applied to monitor the concentrations of ionized pharmaceuticals in living fish, which demonstrated that the device and fiber were suitable for ultrafast in vivo sampling and continuous monitoring. In addition, the bioconcentration factor (BCF) values of the pharmaceuticals were derived in tilapia (Oreochromis mossambicus) for the first time, based on the data of ultrafast in vivo sampling. Therefore, we developed and validated an effective and ultrafast SPME sampling device for in vivo sampling of ionized analytes in living organisms and this state-of-the-art method provides an alternative technique for future in vivo studies.

Identification of Rare Lewis Oligosaccharide Conformers in Aqueous Solution Using Enhanced Sampling Molecular Dynamics.

PubMed

Alibay, Irfan; Burusco, Kepa K; Bruce, Neil J; Bryce, Richard A

2018-03-08

Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free-energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling, and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 μs trajectories; these simulations find a predominance of closed conformer and a range of low-occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the 4 C 1 form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 μs unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.

Enhanced sampling of molecular dynamics simulation of peptides and proteins by double coupling to thermal bath.

PubMed

Chen, Changjun; Huang, Yanzhao; Xiao, Yi

2013-01-01

Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of freedom in the molecule to environment temperature, like dihedrals in generalized coordinates or nonhydrogen atoms in Cartesian coordinate. After applying to ALA dipeptide model, we find that this modified molecular dynamics greatly enhances the sampling behavior in the conformational space and provides more information about the state-to-state transition, while conventional molecular dynamics fails to do so. Moreover, from the results of 16 independent 100 ns simulations by the new method, it shows that trpzip2 has one-half chances to reach the naive state in all the trajectories, which is greatly higher than conventional molecular dynamics. Such an improvement would provide a potential way for searching the conformational space or predicting the most stable states of peptides and proteins.

ENHANCED DAPI STAINING FOR CRYPTOSPORIDIUM IN WATER SAMPLES

EPA Science Inventory

The U.S. Environmental Protection Agency's Method 1623 is used to detect and quantify the presence of {ital Cryptosporidium} spp. oocysts in water. The protocol consists of concentrating a sample, staining this concentrate with a fluorescent antibody, and examining the sample mi...

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis

NASA Astrophysics Data System (ADS)

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-01

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH4+ strategy for ethylene and SO2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO2 from fruits. It was satisfied that trace ethylene and SO2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO2 during the entire LVCC sampling process were proved to be < 4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS.

Large-volume constant-concentration sampling technique coupling with surface-enhanced Raman spectroscopy for rapid on-site gas analysis.

PubMed

Zhang, Zhuomin; Zhan, Yisen; Huang, Yichun; Li, Gongke

2017-08-05

In this work, a portable large-volume constant-concentration (LVCC) sampling technique coupling with surface-enhanced Raman spectroscopy (SERS) was developed for the rapid on-site gas analysis based on suitable derivatization methods. LVCC sampling technique mainly consisted of a specially designed sampling cell including the rigid sample container and flexible sampling bag, and an absorption-derivatization module with a portable pump and a gas flowmeter. LVCC sampling technique allowed large, alterable and well-controlled sampling volume, which kept the concentration of gas target in headspace phase constant during the entire sampling process and made the sampling result more representative. Moreover, absorption and derivatization of gas target during LVCC sampling process were efficiently merged in one step using bromine-thiourea and OPA-NH 4 + strategy for ethylene and SO 2 respectively, which made LVCC sampling technique conveniently adapted to consequent SERS analysis. Finally, a new LVCC sampling-SERS method was developed and successfully applied for rapid analysis of trace ethylene and SO 2 from fruits. It was satisfied that trace ethylene and SO 2 from real fruit samples could be actually and accurately quantified by this method. The minor concentration fluctuations of ethylene and SO 2 during the entire LVCC sampling process were proved to be <4.3% and 2.1% respectively. Good recoveries for ethylene and sulfur dioxide from fruit samples were achieved in range of 95.0-101% and 97.0-104% respectively. It is expected that portable LVCC sampling technique would pave the way for rapid on-site analysis of accurate concentrations of trace gas targets from real samples by SERS. Copyright © 2017 Elsevier B.V. All rights reserved.

Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

PubMed

Rydzewski, J; Nowak, W

2017-12-01

Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand-protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter. Copyright © 2017 Elsevier B.V. All rights reserved.

Use of Body-Mounted Cameras to Enhance Data Collection: An Evaluation of Two Arthropod Sampling Techniques.

PubMed

Hagler, James R; Thompson, Alison L; Stefanek, Melissa A; Machtley, Scott A

2018-03-01

A study was conducted that compared the effectiveness of a sweepnet versus a vacuum suction device for collecting arthropods in cotton. The study differs from previous research in that body-mounted action cameras (B-MACs) were used to record the activity of the person conducting the arthropod collections. The videos produced by the B-MACs were then analyzed with behavioral event recording software to quantify various aspects of the sampling process. The sampler's speed and the number of sampling sweeps or vacuum suctions taken over a fixed distance (12.2 m) of cotton were two of the more significant sampling characteristics quantified for each method. The arthropod counts obtained, combined with the analyses of the videos, enabled us to estimate arthropod sampling efficiency for each technique based on fixed distance, time, and sample unit measurements. Data revealed that the vacuuming was the most precise method for collecting arthropods in the relatively small cotton research plots. However, data also indicates that the sweepnet method would be more efficient for collecting most of the cotton-dwelling arthropod taxa, especially if the sampler could continuously sweep for at least 1 min or ≥80 m (e.g., in larger research plots). The B-MACs are inexpensive and non-cumbersome, the video images generated are outstanding, and they can be archived to provide permanent documentation of a research project. The methods described here could be useful for other types of field-based research to enhance data collection efficiency.

Structural Diversity of Ligand-Binding Androgen Receptors Revealed by Microsecond Long Molecular Dynamics Simulations and Enhanced Sampling.

PubMed

Duan, Mojie; Liu, Na; Zhou, Wenfang; Li, Dan; Yang, Minghui; Hou, Tingjun

2016-09-13

Androgen receptor (AR) plays important roles in the development of prostate cancer (PCa). The antagonistic drugs, which suppress the activity of AR, are widely used in the treatment of PCa. However, the molecular mechanism of antagonism about how ligands affect the structures of AR remains elusive. To better understand the conformational variability of ARs bound with agonists or antagonists, we performed long time unbiased molecular dynamics (MD) simulations and enhanced sampling simulations for the ligand binding domain of AR (AR-LBD) in complex with various ligands. Based on the simulation results, we proposed an allosteric pathway linking ligands and helix 12 (H12) of AR-LBD, which involves the interactions among the ligands and the residues W741, H874, and I899. The interaction pathway provides an atomistic explanation of how ligands affect the structure of AR-LBD. A repositioning of H12 was observed, but it is facilitated by the C-terminal of H12, instead of by the loop between helix 11 (H11) and H12. The bias-exchange metadynamics simulations further demonstrated the above observations. More importantly, the free energy profiles constructed by the enhanced sampling simulations revealed the transition process between the antagonistic form and agonistic form of AR-LBD. Our results would be helpful for the design of more efficient antagonists of AR to combat PCa.

Graphene-enhanced plasmonic nanohole arrays for environmental sensing in aqueous samples

PubMed Central

Genslein, Christa; Hausler, Peter; Kirchner, Eva-Maria; Bierl, Rudolf; Baeumner, Antje J

2016-01-01

The label-free nature of surface plasmon resonance techniques (SPR) enables a fast, specific, and sensitive analysis of molecular interactions. However, detection of highly diluted concentrations and small molecules is still challenging. It is shown here that in contrast to continuous gold films, gold nanohole arrays can significantly improve the performance of SPR devices in angle-dependent measurement mode, as a signal amplification arises from localized surface plasmons at the nanostructures. This leads consequently to an increased sensing capability of molecules bound to the nanohole array surface. Furthermore, a reduced graphene oxide (rGO) sensor surface was layered over the nanohole array. Reduced graphene oxide is a 2D nanomaterial consisting of sp2-hybridized carbon atoms and is an attractive receptor surface for SPR as it omits any bulk phase and therefore allows fast response times. In fact, it was found that nanohole arrays demonstrated a higher shift in the resonance angle of 250–380% compared to a continuous gold film. At the same time the nanohole array structure as characterized by its diameter-to-periodicity ratio had minimal influence on the binding capacity of the sensor surface. As a simple and environmentally highly relevant model, binding of the plasticizer diethyl phthalate (DEP) via π-stacking was monitored on the rGO gold nanohole array realizing a limit of detection of as low as 20 nM. The concentration-dependent signal change was studied with the best performing rGO-modified nanohole arrays. Compared to continuous gold films a diameter-to-periodicity ratio (D/P) of 0.43 lead to a 12-fold signal enhancement. Finally, the effect of environmental waters on the sensor was evaluated using samples from sea, lake and river waters spiked with analytically relevant amounts of DEP during which significant changes in the SPR signal are observed. It is expected that this concept can be successfully transferred to enhance the sensitivity in SPR

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.

MEASUREMENT OF PYRETHROID RESIDUES IN ENVIRONMENTAL AND FOOD SAMPLES BY ENHANCED SOLVENT EXTRACTION/SUPERCRITICAL FLUID EXTRACTION COUPLED WITH GAS CHROMATOGRAPHY-TANDEM MASS SPECTROMETRY

EPA Science Inventory

The abstract summarizes pyrethorid methods development research. It provides a summary of sample preparation and analytical techniques such as supercritical fluid extraction, enhance solvent extraction, gas chromatography and tandem mass spectrometry.

Determination of fluoxetine in pharmaceutical and biological samples based on the silver nanoparticle enhanced fluorescence of fluoxetine-terbium complex.

PubMed

Lotfi, Ali; Manzoori, Jamshid L

2016-11-01

In this study, a simple and sensitive spectrofluorimetric method is presented for the determination of fluoxetine based on the enhancing effect of silver nanoparticles (AgNPs) on the terbium-fluoxetine fluorescence emission. The AgNPs were prepared by a simple reduction method and characterized by UV-Vis spectroscopy and transmission electron microscopy. It was indicated that these AgNPs have a remarkable amplifying effect on the terbium-sensitized fluorescence of fluoxetine. The effects of various parameters such as AgNP and Tb 3+ concentration and the pH of the media were investigated. Under obtained optimal conditions, the fluorescence intensity of the terbium-fluoxetine-AgNP system was enhanced linearly by increasing the concentration of fluoxetine in the range of 0.008 to 19 mg/L. The limit of detection (b + 3s) was 8.3 × 10 -4 mg/L. The interference effects of common species found in real samples were also studied. The method had good linearity, recovery, reproducibility and sensitivity, and was satisfactorily applied for the determination of fluoxetine in tablet formulations, human urine and plasma samples. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

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.

Comparison of hot hydroxylamine hydrochloride and oxalic acid leaching of stream sediment and coated rock samples as anomaly enhancement techniques

USGS Publications Warehouse

Filipek, L.H.; Chao, T.T.; Theobald, P.K.

1982-01-01

A hot hydroxylamine hydrochloride (H-Hxl) extraction in 25% acetic acid is compared with the commonly used oxalic acid extraction as a method of anomaly enhancement for Cu and Zn in samples from two very different metal deposits and climatic environments. Results obtained on minus-80-mesh stream sediments from an area near the Magruder massive sulfide deposit in Lincoln County, Georgia, where the climate is humid subtropical, indicate that H-Hxl enhances the anomaly for Cu by a factor of 2 and for Zn by a factor of 1.5, compared to the oxalic method. Analyses of Fe oxide-coated rock samples from outcrops overlying the North Silver Bell porphyry copper deposit near Tucson, Arizona, where the climate is semi-arid to arid, indicate that both techniques effectively outline the zones of hydrothermal alteration. The H-Hxl extraction can also perform well in high-carbonate or high-clay environments, where other workers have suggested that oxalic acid is not very effective. Therefore, the H-Hxl method is recommended for general exploration use. ?? 1982.

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.

Classification of bacterial samples as negative or positive for a UTI and antibiogram using surface enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Kastanos, Evdokia; Hadjigeorgiou, Katerina; Kyriakides, Alexandros; Pitris, Costas

2011-03-01

Urinary tract infection (UTI) diagnosis requires an overnight culture to identify a sample as positive or negative for a UTI. Additional cultures are required to identify the pathogen responsible for the infection and to test its sensitivity to antibiotics. A rise in ineffective treatments, chronic infections, rising health care costs and antibiotic resistance are some of the consequences of this prolonged waiting period of UTI diagnosis. In this work, Surface Enhanced Raman Spectroscopy (SERS) is used for classifying bacterial samples as positive or negative for UTI. SERS spectra of serial dilutions of E.coli bacteria, isolated from a urine culture, were classified as positive (105-108 cells/ml) or negative (103-104 cells/ml) for UTI after mixing samples with gold nanoparticles. A leave-one-out cross validation was performed using the first two principal components resulting in the correct classification of 82% of all samples. Sensitivity of classification was 88% and specificity was 67%. Antibiotic sensitivity testing was also done using SERS spectra of various species of gram negative bacteria collected 4 hours after exposure to antibiotics. Spectral analysis revealed clear separation between the spectra of samples exposed to ciprofloxacin (sensitive) and amoxicillin (resistant). This study can become the basis for identifying urine samples as positive or negative for a UTI and determining their antibiogram without requiring an overnight culture.

Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins.

PubMed

Walczewska-Szewc, Katarzyna; Deplazes, Evelyne; Corry, Ben

2015-07-14

Adequately sampling the large number of conformations accessible to proteins and other macromolecules is one of the central challenges in molecular dynamics (MD) simulations; this activity can be difficult, even for relatively simple systems. An example where this problem arises is in the simulation of dye-labeled proteins, which are now being widely used in the design and interpretation of Förster resonance energy transfer (FRET) experiments. In this study, MD simulations are used to characterize the motion of two commonly used FRET dyes attached to an immobilized chain of polyproline. Even in this simple system, the dyes exhibit complex behavior that is a mixture of fast and slow motions. Consequently, very long MD simulations are required to sufficiently sample the entire range of dye motion. Here, we compare the ability of enhanced sampling methods to reproduce the behavior of fluorescent labels on proteins. In particular, we compared Accelerated Molecular Dynamics (AMD), metadynamics, Replica Exchange Molecular Dynamics (REMD), and High Temperature Molecular Dynamics (HTMD) to equilibrium MD simulations. We find that, in our system, all of these methods improve the sampling of the dye motion, but the most significant improvement is achieved using REMD.

Final Progress Report for Award DE-FG07-05ID14637.pdf

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

Cathy Dixon

2012-03-09

2004-2011 Final Report for AFCI University Fellowship Program. The goal of this effort was to be supportive of university students and university programs - particularly those students and programs that will help to strengthen the development of nuclear-related fields. The program also supported the stability of the nuclear infrastructure and developed research partnerships that are helping to enlarge the national nuclear science technology base. In this fellowship program, the U.S. Department of Energy sought master's degree students in nuclear, mechanical, or chemical engineering, engineering/applied physics, physics, chemistry, radiochemistry, or fields of science and engineering applicable to the AFCI/Gen IV/GNEP missionsmore » in order to meet future U.S. nuclear program needs. The fellowship program identified candidates and selected full time students of high-caliber who were taking nuclear courses as part of their degree programs. The DOE Academic Program Managers encouraged fellows to pursue summer internships at national laboratories and supported the students with appropriate information so that both the fellows and the nation's nuclear energy objectives were successful.« less

Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations.

PubMed

Otaki, Hiroki; Yagi, Kiyoshi; Ishiuchi, Shun-Ichi; Fujii, Masaaki; Sugita, Yuji

2016-10-06

An accurate theoretical prediction of the vibrational spectrum of polypeptides remains to be a challenge due to (1) their conformational flexibility and (2) non-negligible anharmonic effects. The former makes the search for conformers that contribute to the spectrum difficult, and the latter requires an expensive, quantum mechanical calculation for both electrons and vibrations. Here, we propose a new theoretical approach, which implements an enhanced conformational sampling by the replica-exchange molecular dynamics method, a structural clustering to identify distinct conformations, and a vibrational structure calculation by the second-order vibrational quasi-degenerate perturbation theory (VQDPT2). A systematic mode-selection scheme is developed to reduce the cost of VQDPT2 and the generation of a potential energy surface by the electronic structure calculation. The proposed method is applied to a pentapeptide, SIVSF-NH 2 , for which the infrared spectrum has recently been measured in the gas phase with high resolution in the OH and NH stretching region. The theoretical spectrum of the lowest energy conformer is obtained with a mean absolute deviation of 11.2 cm -1 from the experimental spectrum. Furthermore, the NH stretching frequencies of the five lowest energy conformers are found to be consistent with the literature values measured for small peptides with a similar secondary structure. Therefore, the proposed method is a promising way to analyze the vibrational spectrum of polypeptides.

GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

PubMed

Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

2017-09-30

GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Computer Graphics Simulations of Sampling Distributions.

ERIC Educational Resources Information Center

Gordon, Florence S.; Gordon, Sheldon P.

1989-01-01

Describes the use of computer graphics simulations to enhance student understanding of sampling distributions that arise in introductory statistics. Highlights include the distribution of sample proportions, the distribution of the difference of sample means, the distribution of the difference of sample proportions, and the distribution of sample…

Bennett's acceptance ratio and histogram analysis methods enhanced by umbrella sampling along a reaction coordinate in configurational space.

PubMed

Kim, Ilsoo; Allen, Toby W

2012-04-28

Free energy perturbation, a method for computing the free energy difference between two states, is often combined with non-Boltzmann biased sampling techniques in order to accelerate the convergence of free energy calculations. Here we present a new extension of the Bennett acceptance ratio (BAR) method by combining it with umbrella sampling (US) along a reaction coordinate in configurational space. In this approach, which we call Bennett acceptance ratio with umbrella sampling (BAR-US), the conditional histogram of energy difference (a mapping of the 3N-dimensional configurational space via a reaction coordinate onto 1D energy difference space) is weighted for marginalization with the associated population density along a reaction coordinate computed by US. This procedure produces marginal histograms of energy difference, from forward and backward simulations, with higher overlap in energy difference space, rendering free energy difference estimations using BAR statistically more reliable. In addition to BAR-US, two histogram analysis methods, termed Bennett overlapping histograms with US (BOH-US) and Bennett-Hummer (linear) least square with US (BHLS-US), are employed as consistency and convergence checks for free energy difference estimation by BAR-US. The proposed methods (BAR-US, BOH-US, and BHLS-US) are applied to a 1-dimensional asymmetric model potential, as has been used previously to test free energy calculations from non-equilibrium processes. We then consider the more stringent test of a 1-dimensional strongly (but linearly) shifted harmonic oscillator, which exhibits no overlap between two states when sampled using unbiased Brownian dynamics. We find that the efficiency of the proposed methods is enhanced over the original Bennett's methods (BAR, BOH, and BHLS) through fast uniform sampling of energy difference space via US in configurational space. We apply the proposed methods to the calculation of the electrostatic contribution to the absolute

Multiple injection mode with or without repeated sample injections: Strategies to enhance productivity in countercurrent chromatography.

PubMed

Müller, Marco; Wasmer, Katharina; Vetter, Walter

2018-06-29

Countercurrent chromatography (CCC) is an all liquid based separation technique typically used for the isolation and purification of natural compounds. The simplicity of the method makes it easy to scale up CCC separations from analytical to preparative and even industrial scale. However, scale-up of CCC separations requires two different instruments with varying coil dimensions. Here we developed two variants of the CCC multiple injection mode as an alternative to increase the throughput and enhance productivity of a CCC separation when using only one instrument. The concept is based on the parallel injection of samples at different points in the CCC column system and the simultaneous separation using one pump only. The wiring of the CCC setup was modified by the insertion of a 6-port selection valve, multiple T-pieces and sample loops. Furthermore, the introduction of storage sample loops enabled the CCC system to be used with repeated injection cycles. Setup and advantages of both multiple injection modes were shown by the isolation of the furan fatty acid 11-(3,4-dimethyl-5-pentylfuran-2-yl)-undecanoic acid (11D5-EE) from an ethyl ester oil rich in 4,7,10,13,16,19-docosahexaenoic acid (DHA-EE). 11D5-EE was enriched in one step from 1.9% to 99% purity. The solvent consumption per isolated amount of analyte could be reduced by ∼40% compared to increased throughput CCC and by ∼5% in the repeated multiple injection mode which also facilitated the isolation of the major compound (DHA-EE) in the sample. Copyright © 2018 Elsevier B.V. All rights reserved.

Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin.

PubMed

Orlowski, Slawomir; Nowak, Wieslaw

2007-07-01

Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.

Variational Approach to Enhanced Sampling and Free Energy Calculations

NASA Astrophysics Data System (ADS)

Valsson, Omar; Parrinello, Michele

2014-08-01

The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

Constant pressure-assisted head-column field-amplified sample injection in combination with in-capillary derivatization for enhancing the sensitivity of capillary electrophoresis.

PubMed

Yan, Na; Zhou, Lei; Zhu, Zaifang; Zhang, Huige; Zhou, Ximin; Chen, Xingguo

2009-05-15

In this work, a novel method combining constant pressure-assisted head-column field-amplified sample injection (PA-HC-FASI) with in-capillary derivatization was developed for enhancing the sensitivity of capillary electrophoresis. PA-HC-FASI uses an appropriate positive pressure to counterbalance the electroosmotic flow in the capillary column during electrokinetic injection, while taking advantage of the field amplification in the sample matrix and the water of the "head column". Accordingly, the analytes were stacked at the stationary boundary between water and background electrolyte. After 600s PA-HC-FASI, 4-fluoro-7-nitro-2,1,3-benzoxadiazole as derivatization reagent was injected, followed by an electrokinetic step (5kV, 45s) to enhance the mixing efficiency of analytes and reagent plugs. Standing a specified time of 10min for derivatization reaction under 35 degrees C, then the capillary temperature was cooled to 25 degrees C and the derivatives were immediately separated and determined under 25 degrees C. By investigating the variables of the presented approach in detail, on-line preconcentration, derivatization and separation could be automatically operated in one run and required no modification of current CE commercial instrument. Moreover, the sensitivity enhancement factor of 520 and 800 together with the detection limits of 16.32 and 6.34pg/mL was achieved for model compounds: glufosinate and aminomethylphosphonic acid, demonstrating the high detection sensitivity of the presented method.

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

NASA Astrophysics Data System (ADS)

Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F.

2017-08-01

Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not obtain properties' efficiently because we need to run microseconds or longer simulations using femtosecond time steps. To overcome this time scale barrier, we can use the weighted ensemble (WE) method, a powerful enhanced sampling method that efficiently samples thermodynamic and kinetic properties. However, the WE method requires an appropriate partitioning of phase space into discrete macrostates, which can be problematic when we have a high-dimensional collective space or when little is known a priori about the molecular system. Hence, we developed a new WE-based method, called the "Concurrent Adaptive Sampling (CAS) algorithm," to tackle these issues. The CAS algorithm is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective variables and adaptive macrostates to enhance the sampling in the high-dimensional space. This is especially useful for systems in which we do not know what the right reaction coordinates are, in which case we can use many collective variables to sample conformations and pathways. In addition, a clustering technique based on the committor function is used to accelerate sampling the slowest process in the molecular system. In this paper, we introduce the new method and show results from two-dimensional models and bio-molecules, specifically penta-alanine and a triazine trimer.

Enhanced spot preparation for liquid extractive sampling and analysis

DOEpatents

Van Berkel, Gary J.; King, Richard C.

2015-09-22

A method for performing surface sampling of an analyte, includes the step of placing the analyte on a stage with a material in molar excess to the analyte, such that analyte-analyte interactions are prevented and the analyte can be solubilized for further analysis. The material can be a matrix material that is mixed with the analyte. The material can be provided on a sample support. The analyte can then be contacted with a solvent to extract the analyte for further processing, such as by electrospray mass spectrometry.

Enhanced Wang Landau sampling of adsorbed protein conformations.

PubMed

Radhakrishna, Mithun; Sharma, Sumit; Kumar, Sanat K

2012-03-21

Using computer simulations to model the folding of proteins into their native states is computationally expensive due to the extraordinarily low degeneracy of the ground state. In this paper, we develop an efficient way to sample these folded conformations using Wang Landau sampling coupled with the configurational bias method (which uses an unphysical "temperature" that lies between the collapse and folding transition temperatures of the protein). This method speeds up the folding process by roughly an order of magnitude over existing algorithms for the sequences studied. We apply this method to study the adsorption of intrinsically disordered hydrophobic polar protein fragments on a hydrophobic surface. We find that these fragments, which are unstructured in the bulk, acquire secondary structure upon adsorption onto a strong hydrophobic surface. Apparently, the presence of a hydrophobic surface allows these random coil fragments to fold by providing hydrophobic contacts that were lost in protein fragmentation. © 2012 American Institute of Physics

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.

PubMed

Chen, Yunjie; Roux, Benoît

2015-08-11

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model

PubMed Central

2015-01-01

Molecular dynamics (MD) trajectories based on a classical equation of motion provide a straightforward, albeit somewhat inefficient approach, to explore and sample the configurational space of a complex molecular system. While a broad range of techniques can be used to accelerate and enhance the sampling efficiency of classical simulations, only algorithms that are consistent with the Boltzmann equilibrium distribution yield a proper statistical mechanical computational framework. Here, a multiscale hybrid algorithm relying simultaneously on all-atom fine-grained (FG) and coarse-grained (CG) representations of a system is designed to improve sampling efficiency by combining the strength of nonequilibrium molecular dynamics (neMD) and Metropolis Monte Carlo (MC). This CG-guided hybrid neMD-MC algorithm comprises six steps: (1) a FG configuration of an atomic system is dynamically propagated for some period of time using equilibrium MD; (2) the resulting FG configuration is mapped onto a simplified CG model; (3) the CG model is propagated for a brief time interval to yield a new CG configuration; (4) the resulting CG configuration is used as a target to guide the evolution of the FG system; (5) the FG configuration (from step 1) is driven via a nonequilibrium MD (neMD) simulation toward the CG target; (6) the resulting FG configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-ends momentum reversal prescription is used for the neMD trajectories of the FG system to guarantee that the CG-guided hybrid neMD-MC algorithm obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The enhanced sampling achieved with the method is illustrated with a model system with hindered diffusion and explicit-solvent peptide simulations. Illustrative tests indicate that the method can yield a speedup of about 80 times for the model system and up

Application of surface enhanced Raman scattering and competitive adaptive reweighted sampling on detecting furfural dissolved in transformer oil

NASA Astrophysics Data System (ADS)

Chen, Weigen; Zou, Jingxin; Wan, Fu; Fan, Zhou; Yang, Dingkun

2018-03-01

Detecting the dissolving furfural in mineral oil is an essential technical method to evaluate the ageing condition of oil-paper insulation and the degradation of mechanical properties. Compared with the traditional detection method, Raman spectroscopy is obviously convenient and timesaving in operation. This study explored the method of applying surface enhanced Raman scattering (SERS) on quantitative analysis of the furfural dissolved in oil. Oil solution with different concentration of furfural were prepared and calibrated by high-performance liquid chromatography. Confocal laser Raman spectroscopy (CLRS) and SERS technology were employed to acquire Raman spectral data. Monte Carlo cross validation (MCCV) was used to eliminate the outliers in sample set, then competitive adaptive reweighted sampling (CARS) was developed to select an optimal combination of informative variables that most reflect the chemical properties of concern. Based on selected Raman spectral features, support vector machine (SVM) combined with particle swarm algorithm (PSO) was used to set up a furfural quantitative analysis model. Finally, the generalization ability and prediction precision of the established method were verified by the samples made in lab. In summary, a new spectral method is proposed to quickly detect furfural in oil, which lays a foundation for evaluating the ageing of oil-paper insulation in oil immersed electrical equipment.

Harmonic demodulation and minimum enhancement factors in field-enhanced near-field optical microscopy.

PubMed

Scarpettini, A F; Bragas, A V

2015-01-01

Field-enhanced scanning optical microscopy relies on the design and fabrication of plasmonic probes which had to provide optical and chemical contrast at the nanoscale. In order to do so, the scattering containing the near-field information recorded in a field-enhanced scanning optical microscopy experiment, has to surpass the background light, always present due to multiple interferences between the macroscopic probe and sample. In this work, we show that when the probe-sample distance is modulated with very low amplitude, the higher the harmonic demodulation is, the better the ratio between the near-field signal and the interferometric background results. The choice of working at a given n harmonic is dictated by the experiment when the signal at the n + 1 harmonic goes below the experimental noise. We demonstrate that the optical contrast comes from the nth derivative of the near-field scattering, amplified by the interferometric background. By modelling the far and near field we calculate the probe-sample approach curves, which fit very well the experimental ones. After taking a great amount of experimental data for different probes and samples, we conclude with a table of the minimum enhancement factors needed to have optical contrast with field-enhanced scanning optical microscopy. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling.

PubMed

Mori, Toshifumi; Hamers, Robert J; Pedersen, Joel A; Cui, Qiang

2014-07-17

Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and λ-dynamics is also briefly discussed.

Radar Doppler Processing with Nonuniform Sampling.

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

Doerry, Armin W.

2017-07-01

Conventional signal processing to estimate radar Doppler frequency often assumes uniform pulse/sample spacing. This is for the convenience of t he processing. More recent performance enhancements in processor capability allow optimally processing nonuniform pulse/sample spacing, thereby overcoming some of the baggage that attends uniform sampling, such as Doppler ambiguity and SNR losses due to sidelobe control measures.

Resolution and quality enhancement in terahertz in-line holography by sub-pixel sampling with double-distance reconstruction.

PubMed

Li, Zeyu; Li, Lei; Qin, Yu; Li, Guangbin; Wang, Du; Zhou, Xun

2016-09-05

We demonstrate the enhancement of resolution and image quality in terahertz (THz) lens-free in-line digital holography by sub-pixel sampling with double-distance reconstruction. Multiple sub-pixel shifted low-resolution (LR) holograms recorded by a pyroelectric array detector (100 μm × 100 μm pixel pitch, 124 × 124 pixels) are aligned precisely to synthesize a high-resolution (HR) hologram. By this method, the lateral resolution is no more limited by the pixel pitch, and lateral resolution of 150 μm is obtained, which corresponds to 1.26λ with respect to the illuminating wavelength of 118.8 μm (2.52 THz). Compared with other published works, to date, this is the highest resolution in THz digital holography when considering the illuminating wavelength. In addition, to suppress the twin-image and zero-order artifacts, the complex amplitude distributions of both object and illuminaing background wave fields are reconstructed simultaneously. This is achieved by iterative phase retrieval between the double HR holograms and background images at two recording planes, which does not require any constraints on object plane or a priori knowledge of the sample.

Domain Motion Enhanced (DoME) Model for Efficient Conformational Sampling of Multidomain Proteins.

PubMed

Kobayashi, Chigusa; Matsunaga, Yasuhiro; Koike, Ryotaro; Ota, Motonori; Sugita, Yuji

2015-11-19

Large conformational changes of multidomain proteins are difficult to simulate using all-atom molecular dynamics (MD) due to the slow time scale. We show that a simple modification of the structure-based coarse-grained (CG) model enables a stable and efficient MD simulation of those proteins. "Motion Tree", a tree diagram that describes conformational changes between two structures in a protein, provides information on rigid structural units (domains) and the magnitudes of domain motions. In our new CG model, which we call the DoME (domain motion enhanced) model, interdomain interactions are defined as being inversely proportional to the magnitude of the domain motions in the diagram, whereas intradomain interactions are kept constant. We applied the DoME model in combination with the Go model to simulations of adenylate kinase (AdK). The results of the DoME-Go simulation are consistent with an all-atom MD simulation for 10 μs as well as known experimental data. Unlike the conventional Go model, the DoME-Go model yields stable simulation trajectories against temperature changes and conformational transitions are easily sampled despite domain rigidity. Evidently, identification of domains and their interfaces is useful approach for CG modeling of multidomain proteins.

System for Earth Sample Registration SESAR: Services for IGSN Registration and Sample Metadata Management

NASA Astrophysics Data System (ADS)

Chan, S.; Lehnert, K. A.; Coleman, R. J.

2011-12-01

SESAR, the System for Earth Sample Registration, is an online registry for physical samples collected for Earth and environmental studies. SESAR generates and administers the International Geo Sample Number IGSN, a unique identifier for samples that is dramatically advancing interoperability amongst information systems for sample-based data. SESAR was developed to provide the complete range of registry services, including definition of IGSN syntax and metadata profiles, registration and validation of name spaces requested by users, tools for users to submit and manage sample metadata, validation of submitted metadata, generation and validation of the unique identifiers, archiving of sample metadata, and public or private access to the sample metadata catalog. With the development of SESAR v3, we placed particular emphasis on creating enhanced tools that make metadata submission easier and more efficient for users, and that provide superior functionality for users to manage metadata of their samples in their private workspace MySESAR. For example, SESAR v3 includes a module where users can generate custom spreadsheet templates to enter metadata for their samples, then upload these templates online for sample registration. Once the content of the template is uploaded, it is displayed online in an editable grid format. Validation rules are executed in real-time on the grid data to ensure data integrity. Other new features of SESAR v3 include the capability to transfer ownership of samples to other SESAR users, the ability to upload and store images and other files in a sample metadata profile, and the tracking of changes to sample metadata profiles. In the next version of SESAR (v3.5), we will further improve the discovery, sharing, registration of samples. For example, we are developing a more comprehensive suite of web services that will allow discovery and registration access to SESAR from external systems. Both batch and individual registrations will be possible

Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations

PubMed Central

2016-01-01

Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170

Cryptosporidium Oocyst Detection in Water Samples: Floatation Technique Enhanced with Immunofluorescence Is as Effective as Immunomagnetic Separation Method

PubMed Central

Koompapong, Khuanchai; Sutthikornchai, Chantira

2009-01-01

Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 101, 102, and 103 per 10 µl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 102 per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting. PMID:19967082

Cryptosporidium oocyst detection in water samples: floatation technique enhanced with immunofluorescence is as effective as immunomagnetic separation method.

PubMed

Koompapong, Khuanchai; Sutthikornchai, Chantira; Sukthana, Yowalark

2009-12-01

Cryptosporidium can cause gastrointestinal diseases worldwide, consequently posing public health problems and economic burden. Effective techniques for detecting contaminated oocysts in water are important to prevent and control the contamination. Immunomagnetic separation (IMS) method has been widely employed recently due to its efficiency, but, it is costly. Sucrose floatation technique is generally used for separating organisms by using their different specific gravity. It is effective and cheap but time consuming as well as requiring highly skilled personnel. Water turbidity and parasite load in water sample are additional factors affecting to the recovery rate of those 2 methods. We compared the efficiency of IMS and sucrose floatation methods to recover the spiked Cryptosporidium oocysts in various turbidity water samples. Cryptosporidium oocysts concentration at 1, 10(1), 10(2), and 10(3) per 10 microl were spiked into 3 sets of 10 ml-water turbidity (5, 50, and 500 NTU). The recovery rate of the 2 methods was not different. Oocyst load at the concentration < 10(2) per 10 ml yielded unreliable results. Water turbidity at 500 NTU decreased the recovery rate of both techniques. The combination of sucrose floatation and immunofluorescense assay techniques (SF-FA) showed higher recovery rate than IMS and immunofluorescense assay (IMS-FA). We used this SF-FA to detect Cryptosporidium and Giardia from the river water samples and found 9 and 19 out of 30 (30% and 63.3%) positive, respectively. Our results favored sucrose floatation technique enhanced with immunofluorescense assay for detecting contaminated protozoa in water samples in general laboratories and in the real practical setting.

Strength gradient enhances fatigue resistance of steels

NASA Astrophysics Data System (ADS)

Ma, Zhiwei; Liu, Jiabin; Wang, Gang; Wang, Hongtao; Wei, Yujie; Gao, Huajian

2016-02-01

Steels are heavily used in infrastructure and the transportation industry, and enhancing their fatigue resistance is a major challenge in materials engineering. In this study, by introducing a gradient microstructure into 304 austenitic steel, which is one of the most widely used types of stainless steel, we show that a strength gradient substantially enhances the fatigue life of the material. Pre-notched samples with negative strength gradients in front of the notch’s tip endure many more fatigue cycles than do samples with positive strength gradients during the crack initiation stage, and samples with either type of gradient perform better than do gradient-free samples with the same average yield strength. However, as a crack grows, samples with positive strength gradients exhibit better resistance to fatigue crack propagation than do samples with negative gradients or no gradient. This study demonstrates a simple and promising strategy for using gradient structures to enhance the fatigue resistance of materials and complements related studies of strength and ductility.

Strength gradient enhances fatigue resistance of steels

PubMed Central

Ma, Zhiwei; Liu, Jiabin; Wang, Gang; Wang, Hongtao; Wei, Yujie; Gao, Huajian

2016-01-01

Steels are heavily used in infrastructure and the transportation industry, and enhancing their fatigue resistance is a major challenge in materials engineering. In this study, by introducing a gradient microstructure into 304 austenitic steel, which is one of the most widely used types of stainless steel, we show that a strength gradient substantially enhances the fatigue life of the material. Pre-notched samples with negative strength gradients in front of the notch’s tip endure many more fatigue cycles than do samples with positive strength gradients during the crack initiation stage, and samples with either type of gradient perform better than do gradient-free samples with the same average yield strength. However, as a crack grows, samples with positive strength gradients exhibit better resistance to fatigue crack propagation than do samples with negative gradients or no gradient. This study demonstrates a simple and promising strategy for using gradient structures to enhance the fatigue resistance of materials and complements related studies of strength and ductility. PMID:26907708

Improved sample preparation and counting techniques for enhanced tritium measurement sensitivity

NASA Astrophysics Data System (ADS)

Moran, J.; Aalseth, C.; Bailey, V. L.; Mace, E. K.; Overman, C.; Seifert, A.; Wilcox Freeburg, E. D.

2015-12-01

Tritium (T) measurements offer insight to a wealth of environmental applications including hydrologic tracking, discerning ocean circulation patterns, and aging ice formations. However, the relatively short half-life of T (12.3 years) limits its effective age dating range. Compounding this limitation is the decrease in atmospheric T content by over two orders of magnitude (from 1000-2000 TU in 1962 to < 10 TU currently) since the cessation of above ground nuclear testing in the 1960's. We are developing sample preparation methods coupled to direct counting of T via ultra-low background proportional counters which, when combined, offer improved T measurement sensitivity (~4.5 mmoles of H2 equivalent) and will help expand the application of T age dating to smaller sample sizes linked to persistent environmental questions despite the limitations above. For instance, this approach can be used to T date ~ 2.2 mmoles of CH4 collected from sample-limited systems including microbial communities, soils, or subsurface aquifers and can be combined with radiocarbon dating to distinguish the methane's formation age from C age in a system. This approach can also expand investigations into soil organic C where the improved sensitivity will permit resolution of soil C into more descriptive fractions and provide direct assessments of the stability of specific classes of organic matter in soils environments. We are employing a multiple step sample preparation system whereby organic samples are first combusted with resulting CO2 and H2O being used as a feedstock to synthesize CH4. This CH4 is mixed with Ar and loaded directly into an ultra-low background proportional counter for measurement of T β decay in a shallow underground laboratory. Analysis of water samples requires only the addition of geologic CO2 feedstock with the sample for methane synthesis. The chemical nature of the preparation techniques enable high sample throughput with only the final measurement requiring T decay

Sample processing approach for detection of ricin in surface samples.

PubMed

Kane, Staci; Shah, Sanjiv; Erler, Anne Marie; Alfaro, Teneile

2017-12-01

With several ricin contamination incidents reported over the past decade, rapid and accurate methods are needed for environmental sample analysis, especially after decontamination. A sample processing method was developed for common surface sampling devices to improve the limit of detection and avoid false negative/positive results for ricin analysis. Potential assay interferents from the sample matrix (bleach residue, sample material, wetting buffer), including reference dust, were tested using a Time-Resolved Fluorescence (TRF) immunoassay. Test results suggested that the sample matrix did not cause the elevated background fluorescence sometimes observed when analyzing post-bleach decontamination samples from ricin incidents. Furthermore, sample particulates (80mg/mL Arizona Test Dust) did not enhance background fluorescence or interfere with ricin detection by TRF. These results suggested that high background fluorescence in this immunoassay could be due to labeled antibody quality and/or quantity issues. Centrifugal ultrafiltration devices were evaluated for ricin concentration as a part of sample processing. Up to 30-fold concentration of ricin was observed by the devices, which serve to remove soluble interferents and could function as the front-end sample processing step to other ricin analytical methods. The procedure has the potential to be used with a broader range of environmental sample types and with other potential interferences and to be followed by other ricin analytical methods, although additional verification studies would be required. Published by Elsevier B.V.

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

PubMed

Gill, Samuel C; Lim, Nathan M; Grinaway, Patrick B; Rustenburg, Ariën S; Fass, Josh; Ross, Gregory A; Chodera, John D; Mobley, David L

2018-05-31

Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.

Competition Between Extinction and Enhancement in Surface Enhanced Raman Spectroscopy.

PubMed

van Dijk, Thomas; Sivapalan, Sean T; Devetter, Brent M; Yang, Timothy K; Schulmerich, Matthew V; Murphy, Catherine J; Bhargava, Rohit; Carney, P Scott

2013-04-04

Conjugated metallic nanoparticles are a promising means to achieve ultrasensitive and multiplexed sensing in intact three-dimensional samples, especially for biological applications, via surface enhanced Raman scattering (SERS). We show that enhancement and extinction are linked and compete in a collection of metallic nanoparticles. Counterintuitively, the Raman signal vanishes when nanoparticles are excited at their plasmon resonance, while increasing nanoparticle concentrations at off-resonance excitation sometimes leads to decreased signal. We develop an effective medium theory that explains both phenomena. Optimal choices of excitation wavelength, individual particle enhancement factor and concentrations are indicated. The same processes which give rise to enhancement also lead to increased extinction of both the illumination and the Raman scattered light. Nanoparticles attenuate the incident field (blue) and at the same time provide local enhancement for SERS. Likewise the radiation of the Raman-scattered field (green) is enhanced by the near-by sphere but extinguished by the rest of the spheres in the suspension on propagation.

Metal-enhanced fluorescence exciplex emission.

PubMed

Zhang, Yongxia; Mali, Buddha L; Geddes, Chris D

2012-01-01

In this letter, we report the first observation of metal-enhanced exciplex fluorescence, observed from anthracene in the presence of diethylaniline. Anthracene in the presence of diethylaniline in close proximity to Silver Island Films (SIFs) shows enhanced monomer and exciplex emission as compared to a non-silvered control sample containing no silver nanoparticles. Our findings suggest two complementary methods for the enhancement: (i) surface plasmons can radiate coupled monomer and exciplex fluorescence efficiently, and (ii) enhanced absorption (enhanced electric near-field) further facilitates enhanced emission. Our exciplex studies help us to further understand the complex photophysics of the metal-enhanced fluorescence technology. Copyright © 2011 Elsevier B.V. All rights reserved.

Enhanced Sampling in the Well-Tempered Ensemble

NASA Astrophysics Data System (ADS)

Bonomi, M.; Parrinello, M.

2010-05-01

We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi , J. Comput. Chem. 30, 1615 (2009)JCCHDD0192-865110.1002/jcc.21305]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a Gō model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.

Enhanced sampling in the well-tempered ensemble.

PubMed

Bonomi, M; Parrinello, M

2010-05-14

We introduce the well-tempered ensemble (WTE) which is the biased ensemble sampled by well-tempered metadynamics when the energy is used as collective variable. WTE can be designed so as to have approximately the same average energy as the canonical ensemble but much larger fluctuations. These two properties lead to an extremely fast exploration of phase space. An even greater efficiency is obtained when WTE is combined with parallel tempering. Unbiased Boltzmann averages are computed on the fly by a recently developed reweighting method [M. Bonomi, J. Comput. Chem. 30, 1615 (2009)]. We apply WTE and its parallel tempering variant to the 2d Ising model and to a Gō model of HIV protease, demonstrating in these two representative cases that convergence is accelerated by orders of magnitude.

Polarization Effects on the Cellulose Dissolution in Ionic Liquids: Molecular Dynamics Simulations with Polarization Model and Integrated Tempering Enhanced Sampling Method.

PubMed

Kan, Zigui; Zhu, Qiang; Yang, Lijiang; Huang, Zhixiong; Jin, Biaobing; Ma, Jing

2017-05-04

Conformation of cellulose with various degree of polymerization of n = 1-12 in ionic liquid 1,3-dimethylimidazolium chloride ([C 1 mim]Cl) and the intermolecular interaction between them was studied by means of molecular dynamics (MD) simulations with fixed-charge and charge variable polarizable force fields, respectively. The integrated tempering enhanced sampling method was also employed in the simulations in order to improve the sampling efficiency. Cellulose undergoes significant conformational changes from a gaseous right-hand helical twist along the long axis to a flexible conformation in ionic liquid. The intermolecular interactions between cellulose and ionic liquid were studied by both infrared spectrum measurements and theoretical simulations. Designated by their puckering parameters, the pyranose rings of cellulose oligomers are mainly arranged in a chair conformation. With the increase in the degree of polymerization of cellulose, the boat and skew-boat conformations of cellulose appear in the MD simulations, especially in the simulations with polarization model. The number and population of hydrogen bonds between the cellulose and the chloride anions show that chloride anion is prone to form HBs whenever it approaches the hydroxyl groups of cellulose and, thus, each hydroxyl group is fully hydrogen bonded to the chloride anion. MD simulations with polarization model presented more abundant conformations than that with nonpolarization model. The application of the enhanced sampling method further enlarged the conformational spaces that could be visited by facilitating the system escaping from the local minima. It was found that the electrostatics interactions between the cellulose and ionic liquid contribute more to the total interaction energies than the van der Waals interactions. Although the interaction energy between the cellulose and anion is about 2.9 times that between the cellulose and cation, the role of cation is non-negligible. In contrast

On the enhanced sampling over energy barriers in molecular dynamics simulations.

PubMed

Gao, Yi Qin; Yang, Lijiang

2006-09-21

We present here calculations of free energies of multidimensional systems using an efficient sampling method. The method uses a transformed potential energy surface, which allows an efficient sampling of both low and high energy spaces and accelerates transitions over barriers. It allows efficient sampling of the configuration space over and only over the desired energy range(s). It does not require predetermined or selected reaction coordinate(s). We apply this method to study the dynamics of slow barrier crossing processes in a disaccharide and a dipeptide system.

Sensitivity enhancement and contrasting information provided by free radicals in oriented-sample NMR of bicelle-reconstituted membrane proteins.

PubMed

Tesch, Deanna M; Nevzorov, Alexander A

2014-02-01

Elucidating structure and topology of membrane proteins (MPs) is essential for unveiling functionality of these important biological constituents. Oriented-sample solid-state NMR (OS-NMR) is capable of providing such information on MPs under nearly physiological conditions. However, two dimensional OS-NMR experiments can take several days to complete due to long longitudinal relaxation times combined with the large number of scans to achieve sufficient signal sensitivity in biological samples. Here, free radicals 5-DOXYL stearic acid, TEMPOL, and CAT-1 were added to uniformly (15)N-labeled Pf1 coat protein reconstituted in DMPC/DHPC bicelles, and their effect on the longitudinal relaxation times (T1Z) was investigated. The dramatically shortened T1Z's allowed for the signal gain per unit time to be used for either: (i) up to a threefold reduction of the total experimental time at 99% magnetization recovery or (ii) obtaining up to 74% signal enhancement between the control and radical samples during constant experimental time at "optimal" relaxation delays. In addition, through OS-NMR and high-field EPR studies, free radicals were able to provide positional constraints in the bicelle system, which provide a description of the location of each residue in Pf1 coat protein within the bicellar membranes. This information can be useful in the determination of oligomerization states and immersion depths of larger membrane proteins. Copyright © 2013 Elsevier Inc. All rights reserved.

The Use of NanoTrap Particles as a Sample Enrichment Method to Enhance the Detection of Rift Valley Fever Virus

PubMed Central

Shafagati, Nazly; Narayanan, Aarthi; Baer, Alan; Fite, Katherine; Pinkham, Chelsea; Bailey, Charles; Kashanchi, Fatah; Lepene, Benjamin; Kehn-Hall, Kylene

2013-01-01

Background Rift Valley Fever Virus (RVFV) is a zoonotic virus that is not only an emerging pathogen but is also considered a biodefense pathogen due to the threat it may cause to public health and national security. The current state of diagnosis has led to misdiagnosis early on in infection. Here we describe the use of a novel sample preparation technology, NanoTrap particles, to enhance the detection of RVFV. Previous studies demonstrated that NanoTrap particles lead to both 100 percent capture of protein analytes as well as an improvement of more than 100-fold in sensitivity compared to existing methods. Here we extend these findings by demonstrating the capture and enrichment of viruses. Results Screening of NanoTrap particles indicated that one particle, NT53, was the most efficient at RVFV capture as demonstrated by both qRT-PCR and plaque assays. Importantly, NT53 capture of RVFV resulted in greater than 100-fold enrichment from low viral titers when other diagnostics assays may produce false negatives. NT53 was also capable of capturing and enhancing RVFV detection from serum samples. RVFV that was inactivated through either detergent or heat treatment was still found bound to NT53, indicating the ability to use NanoTrap particles for viral capture prior to transport to a BSL-2 environment. Furthermore, both NP-40-lysed virus and purified RVFV RNA were bound by NT53. Importantly, NT53 protected viral RNA from RNase A degradation, which was not observed with other commercially available beads. Incubation of RVFV samples with NT53 also resulted in increased viral stability as demonstrated through preservation of infectivity at elevated temperatures. Finally, NanoTrap particles were capable of capturing VEEV and HIV, demonstrating the broad applicability of NanoTrap particles for viral diagnostics. Conclusion This study demonstrates NanoTrap particles are capable of capturing, enriching, and protecting RVFV virions. Furthermore, the use of NanoTrap particles

Identification of osteosarcoma-related specific proteins in serum samples using surface-enhanced laser desorption/ionization-time-of-flight mass spectrometry.

PubMed

Gu, Jianli; Li, Jitian; Huang, Manyu; Zhang, Zhiyong; Li, Dongsheng; Song, Guoying; Ding, Xingpo; Li, Wuyin

2014-01-01

Osteosarcoma (OS) is the most common malignant bone tumor. To identify OS-related specific proteins for early diagnosis of OS, a novel approach, surface-enhanced laser desorption/ionization-time-of-flight mass spectrometry (SELDI-TOF-MS) to serum samples from 25 OS patients, 16 osteochondroma, and 26 age-matched normal human volunteers as controls, was performed. Two proteins showed a significantly different expression in OS serum samples from control groups. Proteomic profiles and external leave-one-out cross-validation analysis showed that the correct rate of allocation, the sensitivity, and the specificity of diagnosis were 100%. These two proteins were further identified by searching the EPO-KB database, and one of the proteins identified as Serine rich region profile is involved in various cellular signaling cascades and tumor genesis. The presence of these two proteins in OS patients but absence from premalignant and normal human controls implied that they can be potential biomarkers for early diagnosis of OS.

myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.

PubMed

Kasahara, Kota; Ma, Benson; Goto, Kota; Dasgupta, Bhaskar; Higo, Junichi; Fukuda, Ikuo; Mashimo, Tadaaki; Akiyama, Yutaka; Nakamura, Haruki

2016-01-01

Molecular dynamics (MD) is a promising computational approach to investigate dynamical behavior of molecular systems at the atomic level. Here, we present a new MD simulation engine named "myPresto/omegagene" that is tailored for enhanced conformational sampling methods with a non-Ewald electrostatic potential scheme. Our enhanced conformational sampling methods, e.g. , the virtual-system-coupled multi-canonical MD (V-McMD) method, replace a multi-process parallelized run with multiple independent runs to avoid inter-node communication overhead. In addition, adopting the non-Ewald-based zero-multipole summation method (ZMM) makes it possible to eliminate the Fourier space calculations altogether. The combination of these state-of-the-art techniques realizes efficient and accurate calculations of the conformational ensemble at an equilibrium state. By taking these advantages, myPresto/omegagene is specialized for the single process execution with Graphics Processing Unit (GPU). We performed benchmark simulations for the 20-mer peptide, Trp-cage, with explicit solvent. One of the most thermodynamically stable conformations generated by the V-McMD simulation is very similar to an experimentally solved native conformation. Furthermore, the computation speed is four-times faster than that of our previous simulation engine, myPresto/psygene-G. The new simulator, myPresto/omegagene, is freely available at the following URLs: http://www.protein.osaka-u.ac.jp/rcsfp/pi/omegagene/ and http://presto.protein.osaka-u.ac.jp/myPresto4/.

Communications Relay and Human-Assisted Sample Return from the Deep Space Gateway

NASA Astrophysics Data System (ADS)

Cichan, T.; Hopkins, J. B.; Bierhaus, B.; Murrow, D. W.

2018-02-01

The Deep Space Gateway can enable or enhance exploration of the lunar surface through two capabilities: 1. communications relay, opening up access to the lunar farside, and 2. sample return, enhancing the ability to return large sample masses.

On the Use of Accelerated Molecular Dynamics to Enhance Configurational Sampling in Ab Initio Simulations.

PubMed

Bucher, Denis; Pierce, Levi C T; McCammon, J Andrew; Markwick, Phineus R L

2011-04-12

We have implemented the accelerated molecular dynamics approach (Hamelberg, D.; Mongan, J.; McCammon, J. A. J. Chem. Phys. 2004, 120 (24), 11919) in the framework of ab initio MD (AIMD). Using three simple examples, we demonstrate that accelerated AIMD (A-AIMD) can be used to accelerate solvent relaxation in AIMD simulations and facilitate the detection of reaction coordinates: (i) We show, for one cyclohexane molecule in the gas phase, that the method can be used to accelerate the rate of the chair-to-chair interconversion by a factor of ∼1 × 10(5), while allowing for the reconstruction of the correct canonical distribution of low-energy states; (ii) We then show, for a water box of 64 H(2)O molecules, that A-AIMD can also be used in the condensed phase to accelerate the sampling of water conformations, without affecting the structural properties of the solvent; and (iii) The method is then used to compute the potential of mean force (PMF) for the dissociation of Na-Cl in water, accelerating the convergence by a factor of ∼3-4 compared to conventional AIMD simulations.(2) These results suggest that A-AIMD is a useful addition to existing methods for enhanced conformational and phase-space sampling in solution. While the method does not make the use of collective variables superfluous, it also does not require the user to define a set of collective variables that can capture all the low-energy minima on the potential energy surface. This property may prove very useful when dealing with highly complex multidimensional systems that require a quantum mechanical treatment.

Direct Electrospray Ionization Mass Spectrometric Profiling of Real-World Samples via a Solid Sampling Probe

NASA Astrophysics Data System (ADS)

Yu, Zhan; Chen, Lee Chuin; Mandal, Mridul Kanti; Yoshimura, Kentaro; Takeda, Sen; Hiraoka, Kenzo

2013-10-01

This study presents a novel direct analysis strategy for rapid mass spectrometric profiling of biochemicals in real-world samples via a direct sampling probe (DSP) without sample pretreatments. Chemical modification is applied to a disposable stainless steel acupuncture needle to enhance its surface area and hydrophilicity. After insertion into real-world samples, biofluid can be attached on the DSP surface. With the presence of a high DC voltage and solvent vapor condensing on the tip of the DSP, analyte can be dissolved and electrosprayed. The simplicity in design, versatility in application aspects, and other advantages such as low cost and disposability make this new method a competitive tool for direct analysis of real-world samples.

Enhanced Sampling of Molecular Dynamics Simulations of a Polyalanine Octapeptide: Effects of the Periodic Boundary Conditions on Peptide Conformation.

PubMed

Kasahara, Kota; Sakuraba, Shun; Fukuda, Ikuo

2018-03-08

We investigate the problem of artifacts caused by the periodic boundary conditions (PBC) used in molecular simulation studies. Despite the long history of simulations with PBCs, the existence of measurable artifacts originating from PBCs applied to inherently nonperiodic physical systems remains controversial. Specifically, these artifacts appear as differences between simulations of the same system but with different simulation-cell sizes. Earlier studies have implied that, even in the simple case of a small model peptide in water, sampling inefficiency is a major obstacle to understanding these artifacts. In this study, we have resolved the sampling issue using the replica exchange molecular dynamics (REMD) enhanced-sampling method to explore PBC artifacts. Explicitly solvated zwitterionic polyalanine octapeptides with three different cubic-cells, having dimensions of L = 30, 40, and 50 Å, were investigated to elucidate the differences with 64 replica × 500 ns REMD simulations using the AMBER parm99SB force field. The differences among them were not large overall, and the results for the L = 30 and 40 Å simulations in the conformational free energy landscape were found to be very similar at room temperature. However, a small but statistically significant difference was seen for L = 50 Å. We observed that extended conformations were slightly overstabilized in the smaller systems. The origin of these artifacts is discussed by comparison to an electrostatic calculation method without PBCs.

Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

PubMed Central

Bonomi, Massimiliano; Camilloni, Carlo; Vendruscolo, Michele

2016-01-01

Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide. PMID:27561930

Dynamics and Kinetics Study of "In-Water" Chemical Reactions by Enhanced Sampling of Reactive Trajectories.

PubMed

Zhang, Jun; Yang, Y Isaac; Yang, Lijiang; Gao, Yi Qin

2015-11-12

High potential energy barriers and engagement of solvent coordinates set challenges for in silico studies of chemical reactions, and one is quite commonly limited to study reactions along predefined reaction coordinate(s). A systematic protocol, QM/MM MD simulations using enhanced sampling of reactive trajectories (ESoRT), is established to quantitatively study chemical transitions in complex systems. A number of trajectories for Claisen rearrangement in water and toluene were collected and analyzed, respectively. Evidence was found that the bond making and breaking during this reaction are concerted processes in solutions, preferentially through a chairlike configuration. Water plays an important dynamic role that helps stabilize the transition sate, and the dipole-dipole interaction between water and the solute also lowers the transition barrier. The calculated rate coefficient is consistent with the experimental measurement. Compared with water, the reaction pathway in toluene is "narrower" and the reaction rate is slower by almost three orders of magnitude due to the absence of proper interactions to stabilize the transition state. This study suggests that the "in-water" nature of the Claisen rearrangement in aqueous solution influences its thermodynamics, kinetics, as well as dynamics.

The effect of substrate on electric field enhancement of Tip-enhanced Raman spectroscopy (TERS)

NASA Astrophysics Data System (ADS)

Bahreini, Maryam

2018-01-01

The characterization of materials down to a few-molecule level is a key challenge in nanotechnology. Raman spectroscopy is a powerful method that provides chemical information via nondestructive vibrational fingerprinting. Unfortunately, this method suffers from signal weakness which prevents the study of small quantities. Tip-enhanced Raman spectroscopy (TERS) which combines the chemical sensitivity of Raman spectroscopy (RS) with high spatial resolution of scanning probe microscopy (SPM), provides chemical images of surfaces at the nanometer scale. In this method, irradiation of an SPM tip by a focused laser beam results in enhancement of local electric field via two reasons of localized surface plasmon resonance and lightning rod effect. This enhancement leads to the enhancement in Raman intensity from the sample surface in the vicinity of tip. In all TERS measurements, samples should be located on a substrate. In this paper, the dependence of the electric field enhancement to the substrate has been investigated. In simulations, three-dimensional finite-difference time-domain (3D-FDTD) method is used for numerical solution of Maxwell's equations. Our results show that the electric field enhancement is weak for the tip alone case. Introducing a substrate provides further electric field enhancement via near field electromagnetic dipole-dipole coupling between the tip and substrate. Since the side-illumination geometry is used for laser irradiation, the vertical component of the incident field plays a dominant role in the electric field enhancement. Therefore, the coupling effect between the tip and the substrate is the key contribution to the enhancement. For the case of silicon tip and the gold substrate, the electric field enhancement is improved considerably. There is an optimal tip size for TERS because of the competing effects of the radiation damping and the surface scattering of the tip. The results show the substrate as an effective tool for the

Impact of grey zone sample testing by enzyme-linked immunosorbent assay in enhancing blood safety: Experience at a tertiary care hospital in North India.

PubMed

Solanki, Archana; Singh, Abhay; Chaudhary, Rajendra

2016-01-01

Enzyme-linked immunosorbent assay (ELISA) used for screening blood donors for transfusion transmitted infections (TTIs) can sometimes fail to detect blood donors who are recently infected or possessing the low strength of pathogen. Estimation of a grey zone in ELISA testing and repeat testing of grey zone samples can further help in reducing the risks of TTI in countries where nucleic acid amplification testing for TTIs is not feasible. Grey zone samples with optical density (OD) lying between cut-off OD and 10% below the cut-off OD (cut-off OD × 0.9) were identified during routine ELISA testing. On performing repeat ELISA testing on grey zone samples in duplicate, the samples showing both OD value below grey zone were marked nonreactive, and samples showing one or both OD value in the grey zone were marked indeterminate. The samples on repeat testing showing one or both OD above cut-off value were marked positive. About 119 samples (77 for hepatitis B virus [HBV], 23 for human immunodeficiency virus [HIV], and 19 for hepatitis C virus [HCV]) were found to be in grey zone. On repeat testing of these samples in duplicate, 70 (58.8%) samples (45 for HBV, 12 for HIV, and 13 for HCV) were found to be reactive. Six (5%) samples (four for HBV, one for HIV, and one for HCV) were found to be indeterminate. Seventy donors initially screened negative, were found out to be potentially infectious on repeat grey zone testing. Thus, estimation of grey zone samples with repeat testing can further enhance the safety of blood transfusion.

Equilibrium Sampling in Biomolecular Simulation

PubMed Central

2015-01-01

Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to parallelization to novel uses of hardware. Special focus is placed on classifying algorithms — most of which are underpinned by a few key ideas — in order to understand their fundamental strengths and limitations. Although algorithms have proliferated, progress resulting from novel hardware use appears to be more clear-cut than from algorithms alone, partly due to the lack of widely used sampling measures. PMID:21370970

Investigation of erosion rates of field samples using FDOT's enhanced sediment erosion rate flume (SERF).

DOT National Transportation Integrated Search

2013-09-01

The first part of this project was to enhance and improve the Florida Department of Transportations : Sediment Erosion Rate Flume (SERF) device. Notable improvements include a pump repair, laser : system enhancement, installation of a digital vide...

Sub-microanalysis of solid samples with near-field enhanced atomic emission spectroscopy

NASA Astrophysics Data System (ADS)

Wang, Xiaohua; Liang, Zhisen; Meng, Yifan; Wang, Tongtong; Hang, Wei; Huang, Benli

2018-03-01

A novel approach, which we have chosen to name it as near-field enhanced atomic emission spectroscopy (NFE-AES), was proposed by introducing a scanning tunnelling microscope (STM) system into a laser-induced breakdown spectrometry (LIBS). The near-field enhancement of a laser-illuminated tip was utilized to improve the lateral resolution tremendously. Using the hybrid arrangement, pure metal tablets were analyzed to verify the performance of NFE-AES both in atmosphere and in vacuum. Due to localized surface plasmon resonance (LSPR), the incident electromagnetic field is enhanced and confined at the apex of tip, resulting in sub-micron scale ablation and elemental emission signal. We discovered that the signal-to-noise ratio (SNR) and the spectral resolution obtained in vacuum condition are better than those acquired in atmospheric condition. The quantitative capability of NFE-AES was demonstrated by analyzing Al and Pb in Cu matrix, respectively. Submicron-sized ablation craters were achieved by performing NFE-AES on a Si wafer with an Al film, and the spectroscopic information from a crater of 650 nm diameter was successfully obtained. Due to its advantage of high lateral resolution, NFE-AES imaging of micro-patterned Al lines on an integrated circuit of a SIM card was demonstrated with a sub-micron lateral resolution. These results reveal the potential of the NFE-AES technique in sub-microanalysis of solids, opening an opportunity to map chemical composition at sub-micron scale.

Revealing the favorable dissociation pathway of type II kinase inhibitors via enhanced sampling simulations and two-end-state calculations.

PubMed

Sun, Huiyong; Tian, Sheng; Zhou, Shunye; Li, Youyong; Li, Dan; Xu, Lei; Shen, Mingyun; Pan, Peichen; Hou, Tingjun

2015-02-13

How does a type II inhibitor bind to/unbind from a kinase target is still a confusing question because the small molecule occupies both the ATP pocket and the allosteric pocket of the kinase binding site. Here, by using enhanced sampling simulations (umbrella sampling, US) and two-end-state free energy calculations (MM/GSBA), we systemically studied the dissociation processes of two distinct small molecules escaping from the binding pocket of p38 MAP kinase through the allosteric channel and the ATP channel. The results show that the unbinding pathways along the allosteric channel have much lower PMF depths than those along the ATP channel, suggesting that the allosteric channel is more favorable for the dissociations of the two inhibitors and thereby supporting the general understanding that the largest channel of a target is usually the entry/exit pathway for the binding/dissociation of small molecules. Interestingly, the MM/GBSA approach yielded similar PMF profiles compared with those based on US, a much time consuming approach, indicating that for a general study, such as detecting the important transition state of a ligand binding/unbinding process, MM/GBSA may be a feasible choice.

Sensitivity of nonuniform sampling NMR.

PubMed

Palmer, Melissa R; Suiter, Christopher L; Henry, Geneive E; Rovnyak, James; Hoch, Jeffrey C; Polenova, Tatyana; Rovnyak, David

2015-06-04

Many information-rich multidimensional experiments in nuclear magnetic resonance spectroscopy can benefit from a signal-to-noise ratio (SNR) enhancement of up to about 2-fold if a decaying signal in an indirect dimension is sampled with nonconsecutive increments, termed nonuniform sampling (NUS). This work provides formal theoretical results and applications to resolve major questions about the scope of the NUS enhancement. First, we introduce the NUS Sensitivity Theorem in which any decreasing sampling density applied to any exponentially decaying signal always results in higher sensitivity (SNR per square root of measurement time) than uniform sampling (US). Several cases will illustrate this theorem and show that even conservative applications of NUS improve sensitivity by useful amounts. Next, we turn to a serious limitation of uniform sampling: the SNR by US decreases for extending evolution times, and thus total experimental times, beyond 1.26T2 (T2 = signal decay constant). Thus, SNR and resolution cannot be simultaneously improved by extending US beyond 1.26T2. We find that NUS can eliminate this constraint, and we introduce the matched NUS SNR Theorem: an exponential sampling density matched to the signal decay always improves the SNR with additional evolution time. Though proved for a specific case, broader classes of NUS densities also improve SNR with evolution time. Applications of these theoretical results are given for a soluble plant natural product and a solid tripeptide (u-(13)C,(15)N-MLF). These formal results clearly demonstrate the inadequacies of applying US to decaying signals in indirect nD-NMR dimensions, supporting a broader adoption of NUS.

Driven Boson Sampling.

PubMed

Barkhofen, Sonja; Bartley, Tim J; Sansoni, Linda; Kruse, Regina; Hamilton, Craig S; Jex, Igor; Silberhorn, Christine

2017-01-13

Sampling the distribution of bosons that have undergone a random unitary evolution is strongly believed to be a computationally hard problem. Key to outperforming classical simulations of this task is to increase both the number of input photons and the size of the network. We propose driven boson sampling, in which photons are input within the network itself, as a means to approach this goal. We show that the mean number of photons entering a boson sampling experiment can exceed one photon per input mode, while maintaining the required complexity, potentially leading to less stringent requirements on the input states for such experiments. When using heralded single-photon sources based on parametric down-conversion, this approach offers an ∼e-fold enhancement in the input state generation rate over scattershot boson sampling, reaching the scaling limit for such sources. This approach also offers a dramatic increase in the signal-to-noise ratio with respect to higher-order photon generation from such probabilistic sources, which removes the need for photon number resolution during the heralding process as the size of the system increases.

Characterization of Metabolic, Diffusion, and Perfusion Properties in GBM: Contrast-Enhancing versus Non-Enhancing Tumor.

PubMed

Autry, Adam; Phillips, Joanna J; Maleschlijski, Stojan; Roy, Ritu; Molinaro, Annette M; Chang, Susan M; Cha, Soonmee; Lupo, Janine M; Nelson, Sarah J

2017-12-01

Although the contrast-enhancing (CE) lesion on T 1 -weighted MR images is widely used as a surrogate for glioblastoma (GBM), there are also non-enhancing regions of infiltrative tumor within the T 2 -weighted lesion, which elude radiologic detection. Because non-enhancing GBM (Enh-) challenges clinical patient management as latent disease, this study sought to characterize ex vivo metabolic profiles from Enh- and CE GBM (Enh+) samples, alongside histological and in vivo MR parameters, to assist in defining criteria for estimating total tumor burden. Fifty-six patients with newly diagnosed GBM received a multi-parametric pre-surgical MR examination. Targets for obtaining image-guided tissue samples were defined based on in vivo parameters that were suspicious for tumor. The actual location from where tissue samples were obtained was recorded, and half of each sample was analyzed for histopathology while the other half was scanned using HR-MAS spectroscopy. The Enh+ and Enh- tumor samples demonstrated comparable mitotic activity, but also significant heterogeneity in microvascular morphology. Ex vivo spectroscopic parameters indicated similar levels of total choline and N-acetylaspartate between these contrast-based radiographic subtypes of GBM, and characteristic differences in the levels of myo-inositol, creatine/phosphocreatine, and phosphoethanolamine. Analysis of in vivo parameters at the sample locations were consistent with histological and ex vivo metabolic data. The similarity between ex vivo levels of choline and NAA, and between in vivo levels of choline, NAA and nADC in Enh+ and Enh- tumor, indicate that these parameters can be used in defining non-invasive metrics of total tumor burden for patients with GBM. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Drone inflight mixing of biochemical samples.

PubMed

Katariya, Mayur; Chung, Dwayne Chung Kim; Minife, Tristan; Gupta, Harshit; Zahidi, Alifa Afiah Ahmad; Liew, Oi Wah; Ng, Tuck Wah

2018-03-15

Autonomous systems for sample transport to the laboratory for analysis can be improved in terms of timeliness, cost and error mitigation in the pre-analytical testing phase. Drones have been reported for outdoor sample transport but incorporating devices on them to attain homogenous mixing of reagents during flight to enhance sample processing timeliness is limited by payload issues. It is shown here that flipping maneuvers conducted with quadcopters are able to facilitate complete and gentle mixing. This capability incorporated during automated sample transport serves to address an important factor contributing to pre-analytical variability which ultimately impacts on test result reliability. Copyright © 2018 Elsevier Inc. All rights reserved.

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins.

PubMed

Andersen, Ole Juul; Grouleff, Julie; Needham, Perri; Walker, Ross C; Jensen, Frank

2015-11-19

Current enhanced sampling molecular dynamics methods for studying large conformational changes in proteins suffer from certain limitations. These include, among others, the need for user defined collective variables, the prerequisite of both start and end point structures of the conformational change, and the need for a priori knowledge of the amount by which to boost specific parts of the potential. In this paper, a framework is proposed for a molecular dynamics method for studying ligand-induced conformational changes, in which the nonbonded interactions between the ligand and the protein are used to calculate a biasing force. The method requires only a single input structure, and does not entail the use of collective variables. We provide a proof-of-concept for accelerating conformational changes in three simple test molecules, as well as promising results for two proteins known to undergo domain closure upon ligand binding. For the ribose-binding protein, backbone root-mean-square deviations as low as 0.75 Å compared to the crystal structure of the closed conformation are obtained within 50 ns simulations, whereas no domain closures are observed in unbiased simulations. A skewed closed structure is obtained for the glutamine-binding protein at high bias values, indicating that specific protein-ligand interactions might suppress important protein-protein interactions.

Combined Dynamic Contrast Enhanced Liver MRI and MRA Using Interleaved Variable Density Sampling

PubMed Central

Rahimi, Mahdi Salmani; Korosec, Frank R.; Wang, Kang; Holmes, James H.; Motosugi, Utaroh; Bannas, Peter; Reeder, Scott B.

2014-01-01

Purpose To develop and evaluate a method for volumetric contrast-enhanced MR imaging of the liver, with high spatial and temporal resolutions, for combined dynamic imaging and MR angiography using a single injection of contrast. Methods An interleaved variable density (IVD) undersampling pattern was implemented in combination with a real-time-triggered, time-resolved, dual-echo 3D spoiled gradient echo sequence. Parallel imaging autocalibration lines were acquired only once during the first time-frame. Imaging was performed in ten subjects with focal nodular hyperplasia (FNH) and compared with their clinical MRI. The angiographic phase of the proposed method was compared to a dedicated MR angiogram acquired during a second injection of contrast. Results A total of 21 FNH, 3 cavernous hemangiomas, and 109 arterial segments were visualized in 10 subjects. The temporally-resolved images depicted the characteristic arterial enhancement pattern of the lesions with a 4 s update rate. Images were graded as having significantly higher quality compared to the clinical MRI. Angiograms produced from the IVD method provided non-inferior diagnostic assessment compared to the dedicated MRA. Conclusion Using an undersampled IVD imaging method, we have demonstrated the feasibility of obtaining high spatial and temporal resolution dynamic contrast-enhanced imaging and simultaneous MRA of the liver. PMID:24639130

Research-Grade 3D Virtual Astromaterials Samples: Novel Visualization of NASA's Apollo Lunar Samples and Antarctic Meteorite Samples to Benefit Curation, Research, and Education

NASA Technical Reports Server (NTRS)

Blumenfeld, E. H.; Evans, C. A.; Oshel, E. R.; Liddle, D. A.; Beaulieu, K. R.; Zeigler, R. A.; Righter, K.; Hanna, R. D.; Ketcham, R. A.

2017-01-01

NASA's vast and growing collections of astromaterials are both scientifically and culturally significant, requiring unique preservation strategies that need to be recurrently updated to contemporary technological capabilities and increasing accessibility demands. New technologies have made it possible to advance documentation and visualization practices that can enhance conservation and curation protocols for NASA's Astromaterials Collections. Our interdisciplinary team has developed a method to create 3D Virtual Astromaterials Samples (VAS) of the existing collections of Apollo Lunar Samples and Antarctic Meteorites. Research-grade 3D VAS will virtually put these samples in the hands of researchers and educators worldwide, increasing accessibility and visibility of these significant collections. With new sample return missions on the horizon, it is of primary importance to develop advanced curation standards for documentation and visualization methodologies.

Molecular dynamics coupled with a virtual system for effective conformational sampling.

PubMed

Hayami, Tomonori; Kasahara, Kota; Nakamura, Haruki; Higo, Junichi

2018-07-15

An enhanced conformational sampling method is proposed: virtual-system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free-energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Active sampling technique to enhance chemical signature of buried explosives

NASA Astrophysics Data System (ADS)

Lovell, John S.; French, Patrick D.

2004-09-01

Deminers and dismounted countermine engineers commonly use metal detectors, ground penetrating radar and probes to locate mines. Many modern landmines have a very low metal content, which severely limits the effectiveness of metal detectors. Canines have also been used for landmine detection for decades. Experiments have shown that canines smell the explosives which are known to leak from most types of landmines. The fact that dogs can detect landmines indicates that vapor sensing is a viable approach to landmine detection. Several groups are currently developing systems to detect landmines by "sniffing" for the ultra-trace explosive vapors above the soil. The amount of material that is available to passive vapor sensing systems is limited to no more than the vapor in equilibrium with the explosive related chemicals (ERCs) distributed in the surface soils over and near the landmine. The low equilibrium vapor pressure of TNT in the soil/atmosphere boundary layer and the limited volume of the boundary layer air imply that passive chemical vapor sensing systems require sensitivities in the picogram range, or lower. ADA is working to overcome many of the limitations of passive sampling methods, by the use of an active sampling method that employs a high-powered (1,200+ joules) strobe lamp to create a highly amplified plume of vapor and/or ERC-bearing fine particulates. Initial investigations have demonstrated that this approach can amplify the detectability of TNT by two or three orders of magnitude. This new active sampling technique could be used with any suitable explosive sensor.

Silver nanoparticles enhanced flow injection chemiluminescence determination of gatifloxacin in pharmaceutical formulation and spiked urine sample.

PubMed

Wabaidur, Saikh mohammad; Alam, Seikh Mafiz; Alothman, Zeid A; Mohsin, Kazi

2015-06-05

Silver nanoparticles have been utilized for the enhanced chemiluminogenic estimation of fluoroquinolone antibiotic gatifloxacin. It has been found that the weak chemiluminescence intensity produced from the reaction between calcein and KMnO4 can further be strengthened by the addition of silver nanoparticles in the presence of gatifloxacin. This phenomenon has been exploited to the quantitative determination of gatifloxacin. Under the optimum experimental conditions, the calibration curves are linear over the range of 8.9×10(-9)-4.0×10(-6) M, while the limits of detections were found to be 2.6×10(-9) M with correlation coefficient value (r(2)) 0.9999. The relative standard deviation calculated from six replicate measurements (1.0×10(-4) M gatifloxacin) was 1.70%. The method was applied to pharmaceutical preparations and the results obtained were in reasonable agreement with the amount labeled on the formulations. The proposed method was also used for the determination of gatifloxacin in spiked urine samples with satisfactory results. No interference effects from some common excipients used in pharmaceutical preparations have been found. Copyright © 2015 Elsevier B.V. All rights reserved.

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations.

PubMed

Bernetti, Mattia; Masetti, Matteo; Pietrucci, Fabio; Blackledge, Martin; Jensen, Malene Ringkjobing; Recanatini, Maurizio; Mollica, Luca; Cavalli, Andrea

2017-10-19

Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome. Being able to interact with different molecular targets, they participate in many physiological and pathological activities. However, due to their intrinsically heterogeneous nature, determining the equilibrium properties of IDPs is still a challenge for biophysics. Herein, we applied state-of-the-art enhanced sampling methods to Sev N TAIL , a test case of IDPs, and constructed a bin-based kinetic model to unveil the underlying kinetics. To validate our simulation strategy, we compared the predicted NMR properties against available experimental data. Our simulations reveal a rough free-energy surface comprising multiple local minima, which are separated by low energy barriers. Moreover, we identified interconversion rates between the main kinetic states, which lie in the sub-μs time scales, as suggested in previous works for Sev N TAIL . Therefore, the emerging picture is in agreement with the atomic-level properties possessed by the free IDP in solution. By providing both a thermodynamic and kinetic characterization of this IDP test case, our study demonstrates how computational methods can be effective tools for studying this challenging class of proteins.

Surface-enhanced Raman scattering detection of ammonium nitrate samples fabricated using drop-on-demand inkjet technology.

PubMed

Farrell, Mikella E; Holthoff, Ellen L; Pellegrino, Paul M

2014-01-01

The United States Army and the first responder community are increasingly focusing efforts on energetic materials detection and identification. Main hazards encountered in theater include homemade explosives and improvised explosive devices, in part fabricated from simple components like ammonium nitrate (AN). In order to accurately detect and identify these unknowns (energetic or benign), fielded detection systems must be accurately trained using well-understood universal testing substrates. These training substrates must contain target species at known concentrations and recognized polymorphic phases. Ammonium nitrate is an explosive precursor material that demonstrates several different polymorphic phases dependent upon how the material is deposited onto testing substrates. In this paper, known concentrations of AN were uniformly deposited onto commercially available surface-enhanced Raman scattering (SERS) substrates using a drop-on-demand inkjet printing system. The phase changes observed after the deposition of AN under several solvent conditions are investigated. Characteristics of the collected SERS spectra of AN are discussed, and it is demonstrated that an understanding of the exact nature of the AN samples deposited will result in an increased ability to accurately and reliably "train" hazard detection systems.

Optimizing laser crater enhanced Raman scattering spectroscopy

NASA Astrophysics Data System (ADS)

Lednev, V. N.; Sdvizhenskii, P. A.; Grishin, M. Ya.; Fedorov, A. N.; Khokhlova, O. V.; Oshurko, V. B.; Pershin, S. M.

2018-05-01

The laser crater enhanced Raman scattering (LCERS) spectroscopy technique has been systematically studied for chosen sampling strategy and influence of powder material properties on spectra intensity enhancement. The same nanosecond pulsed solid state Nd:YAG laser (532 nm, 10 ns, 0.1-1.5 mJ/pulse) was used for laser crater production and Raman scattering experiments for L-aspartic acid powder. Increased sampling area inside crater cavity is the key factor for Raman signal improvement for the LCERS technique, thus Raman signal enhancement was studied as a function of numerous experimental parameters including lens-to-sample distance, wavelength (532 and 1064 nm) and laser pulse energy utilized for crater production. Combining laser pulses of 1064 and 532 nm wavelengths for crater ablation was shown to be an effective way for additional LCERS signal improvement. Powder material properties (particle size distribution, powder compactness) were demonstrated to affect LCERS measurements with better results achieved for smaller particles and lower compactness.

Investigation on tip enhanced Raman spectra of graphene

NASA Astrophysics Data System (ADS)

Li, Xinjuan; Liu, Yanqi; Zeng, Zhuo; Wang, Peijie; Fang, Yan; Zhang, Lisheng

2018-02-01

Tip-enhanced Raman scattering (TERS) is a promising analytical approach for some two-dimensional materials and offers the possibility to correlate imaging and chemical data. Tip-enhanced Raman spectra of graphene are discussed in some details, including substrate, gap between tip-apex and sample surface as well as Ag-nanowire. The TERS spectra give special emphasis to the possibility of TERS tip to induce a large number of defects only while got the tip attached to sample surface. Then the dependence of the TERS spectra of graphene and gap between the probe tip and sample surface was studied, and distribution features of electromagnetic (EM) field around tip were also simulated by finite-difference time-domain (FDTD). The Raman signal enhancement of graphene was further discussed with respect to experimental data. Furthermore, the Ag-nanowire as a nano-antenna could significantly enhance the weak Raman signal of D-band of monolayer graphene is shown, and the TERS spectra of graphene with regard to different regions of Ag-nanowires (endpoints, body) were obtained toward investigating into the distribution of electromagnetic field.

U-2012: An improved Lowry protein assay, insensitive to sample color, offering reagent stability and enhanced sensitivity.

PubMed

Upreti, Girish C; Wang, Yanming; Finn, Alona; Sharrock, Abigail; Feisst, Nicholas; Davy, Marcus; Jordan, Robert B

2012-03-01

Traditional colorimetric protein assays such as Biuret, Lowry, and modified Lowry (U-1988) are unsuitable for colored biological samples. Here we describe an improved Lowry protein assay (U-2012), which utilizes stable reagents and offers enhanced sensitivity over the U-1988 assay. U-2012 circumvents interference from colored pigments and other substances (for example sugars) bound to perchloric acid (PCA) precipitated proteins by hydrogen peroxide (H2O2) induced oxidation at 50°C. Unused hydrogen peroxide is neutralized with sodium pyruvate before protein estimation for a stable end color. The U-2012 assay is carried out on the PCA precipitated protein pellet after neutralization (with Na2CO3 plus NaOH), solubilization (in Triton-NaCl), decolorization (by H2O2) and pyruvate treatment. Protein contents in red wine and homogenates of beetroot and blueberry are calculated from standard curves established for various proteins and generated using a rectangular hyperbola with parameters estimated with Microsoft Excel's Solver add-in. The U-2012 protein assay represents an improvement over U-1988 and gives a more accurate estimation of protein content.

Optimizing laser crater enhanced Raman spectroscopy.

PubMed

Lednev, V N; Sdvizhenskii, P A; Grishin, M Ya; Filichkina, V A; Shchegolikhin, A N; Pershin, S M

2018-03-20

Raman signal enhancement by laser crater production was systematically studied for 785 nm continuous wave laser pumping. Laser craters were produced in L-aspartic acid powder by a nanosecond pulsed solid state neodymium-doped yttrium aluminum garnet laser (532 nm, 8 ns, 1 mJ/pulse), while Raman spectra were then acquired by using a commercial spectrometer with 785 nm laser beam pumping. The Raman signal enhancement effect was studied in terms of the number of ablating pulses used, the lens-to-sample distance, and the crater-center-laser-spot offset. The influence of the experiment parameters on Raman signal enhancement was studied for different powder materials. Maximum Raman signal enhancement reached 11 fold for loose powders but decreased twice for pressed tablets. Raman signal enhancement was demonstrated for several diverse powder materials like gypsum or ammonium nitrate with better results achieved for the samples tending to give narrow and deep craters upon the laser ablation stage. Alternative ways of cavity production (steel needle tapping and hole drilling) were compared with the laser cratering technique in terms of Raman signal enhancement. Drilling was found to give the poorest enhancement of the Raman signal, while both laser ablation and steel needle tapping provided comparable results. Here, we have demonstrated for the first time, to the best of our knowledge, that a Raman signal can be enhanced 10 fold with the aid of simple cavity production by steel needle tapping in rough highly reflective materials. Though laser crater enhancement Raman spectroscopy requires an additional pulsed laser, this technique is more appropriate for automatization compared to the needle tapping approach.

Exhaustively sampling peptide adsorption with metadynamics.

PubMed

Deighan, Michael; Pfaendtner, Jim

2013-06-25

Simulating the adsorption of a peptide or protein and obtaining quantitative estimates of thermodynamic observables remains challenging for many reasons. One reason is the dearth of molecular scale experimental data available for validating such computational models. We also lack simulation methodologies that effectively address the dual challenges of simulating protein adsorption: overcoming strong surface binding and sampling conformational changes. Unbiased classical simulations do not address either of these challenges. Previous attempts that apply enhanced sampling generally focus on only one of the two issues, leaving the other to chance or brute force computing. To improve our ability to accurately resolve adsorbed protein orientation and conformational states, we have applied the Parallel Tempering Metadynamics in the Well-Tempered Ensemble (PTMetaD-WTE) method to several explicitly solvated protein/surface systems. We simulated the adsorption behavior of two peptides, LKα14 and LKβ15, onto two self-assembled monolayer (SAM) surfaces with carboxyl and methyl terminal functionalities. PTMetaD-WTE proved effective at achieving rapid convergence of the simulations, whose results elucidated different aspects of peptide adsorption including: binding free energies, side chain orientations, and preferred conformations. We investigated how specific molecular features of the surface/protein interface change the shape of the multidimensional peptide binding free energy landscape. Additionally, we compared our enhanced sampling technique with umbrella sampling and also evaluated three commonly used molecular dynamics force fields.

Rapid determination of actinides in seawater samples

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

Maxwell, Sherrod L.; Culligan, Brian K.; Hutchison, Jay B.

2014-03-09

A new rapid method for the determination of actinides in seawater samples has been developed at the Savannah River National Laboratory. The actinides can be measured by alpha spectrometry or inductively-coupled plasma mass spectrometry. The new method employs novel pre-concentration steps to collect the actinide isotopes quickly from 80 L or more of seawater. Actinides are co-precipitated using an iron hydroxide co-precipitation step enhanced with Ti +3 reductant, followed by lanthanum fluoride co-precipitation. Stacked TEVA Resin and TRU Resin cartridges are used to rapidly separate Pu, U, and Np isotopes from seawater samples. TEVA Resin and DGA Resin were usedmore » to separate and measure Pu, Am and Cm isotopes in seawater volumes up to 80 L. This robust method is ideal for emergency seawater samples following a radiological incident. It can also be used, however, for the routine analysis of seawater samples for oceanographic studies to enhance efficiency and productivity. In contrast, many current methods to determine actinides in seawater can take 1–2 weeks and provide chemical yields of ~30–60 %. This new sample preparation method can be performed in 4–8 h with tracer yields of ~85–95 %. By employing a rapid, robust sample preparation method with high chemical yields, less seawater is needed to achieve lower or comparable detection limits for actinide isotopes with less time and effort.« less

Dynamic nuclear polarization in solid samples by electrical-discharge-induced radicals

NASA Astrophysics Data System (ADS)

Katz, Itai; Blank, Aharon

2015-12-01

Dynamic nuclear polarization (DNP) is a method for enhancing nuclear magnetic resonance (NMR) signals that has many potential applications in chemistry and medicine. Traditionally, DNP signal enhancement is achieved through the use of exogenous radicals mixed in a solution with the molecules of interest. Here we show that proton DNP signal enhancements can be obtained for solid samples without the use of solvent and exogenous radicals. Radicals are generated primarily on the surface of a solid sample using electrical discharges. These radicals are found suitable for DNP. They are stable under moderate vacuum conditions, yet readily annihilate upon compound dissolution or air exposure. This feature makes them attractive for use in medical applications, where the current variety of radicals used for DNP faces regulatory problems. In addition, this solvent-free method may be found useful for analytical NMR of solid samples which cannot tolerate solvents, such as certain pharmaceutical products.

Enhancing local health department disaster response capacity with rapid community needs assessments: validation of a computerized program for binary attribute cluster sampling.

PubMed

Groenewold, Matthew R

2006-01-01

Local health departments are among the first agencies to respond to disasters or other mass emergencies. However, they often lack the ability to handle large-scale events. Plans including locally developed and deployed tools may enhance local response. Simplified cluster sampling methods can be useful in assessing community needs after a sudden-onset, short duration event. Using an adaptation of the methodology used by the World Health Organization Expanded Programme on Immunization (EPI), a Microsoft Access-based application for two-stage cluster sampling of residential addresses in Louisville/Jefferson County Metro, Kentucky was developed. The sampling frame was derived from geographically referenced data on residential addresses and political districts available through the Louisville/Jefferson County Information Consortium (LOJIC). The program randomly selected 30 clusters, defined as election precincts, from within the area of interest, and then, randomly selected 10 residential addresses from each cluster. The program, called the Rapid Assessment Tools Package (RATP), was tested in terms of accuracy and precision using data on a dichotomous characteristic of residential addresses available from the local tax assessor database. A series of 30 samples were produced and analyzed with respect to their precision and accuracy in estimating the prevalence of the study attribute. Point estimates with 95% confidence intervals were calculated by determining the proportion of the study attribute values in each of the samples and compared with the population proportion. To estimate the design effect, corresponding simple random samples of 300 addresses were taken after each of the 30 cluster samples. The sample proportion fell within +/-10 absolute percentage points of the true proportion in 80% of the samples. In 93.3% of the samples, the point estimate fell within +/-12.5%, and 96.7% fell within +/-15%. All of the point estimates fell within +/-20% of the true

Enhancing Employee Skills.

ERIC Educational Resources Information Center

1999

This document contains four symposium papers on enhancing employee skills. "The Effect of Study Skills Training Intervention on United States Air Force Aeromedical Apprentices" (John C. Griffith) demonstrates how study skills intervention resulted in a significant increase in the end-of-course scores of a sample of 90 randomly selected Air Force…

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

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

Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F.

Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run microseconds or longer simulations using femtoseconds time steps. While there are several existing methods to overcome this timescale barrier and efficiently sample thermodynamic and/or kinetic properties, problems remain in regard to being able to sample un- known systems, deal with high-dimensional space of collective variables, and focus the computational effort on slow timescales. Hence, a new sampling method, called the “Concurrent Adaptive Sampling (CAS) algorithm,”more » has been developed to tackle these three issues and efficiently obtain conformations and pathways. The method is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective vari- ables and uses macrostates (a partition of the collective variable space) to enhance the sampling. The exploration is done by running a large number of short simula- tions, and a clustering technique is used to accelerate the sampling. In this paper, we introduce the new methodology and show results from two-dimensional models and bio-molecules, such as penta-alanine and triazine polymer« less

Dynamics Sampling in Transition Pathway Space.

PubMed

Zhou, Hongyu; Tao, Peng

2018-01-09

The minimum energy pathway contains important information describing the transition between two states on a potential energy surface (PES). Chain-of-states methods were developed to efficiently calculate minimum energy pathways connecting two stable states. In the chain-of-states framework, a series of structures are generated and optimized to represent the minimum energy pathway connecting two states. However, multiple pathways may exist connecting two existing states and should be identified to obtain a full view of the transitions. Therefore, we developed an enhanced sampling method, named as the direct pathway dynamics sampling (DPDS) method, to facilitate exploration of a PES for multiple pathways connecting two stable states as well as addition minima and their associated transition pathways. In the DPDS method, molecular dynamics simulations are carried out on the targeting PES within a chain-of-states framework to directly sample the transition pathway space. The simulations of DPDS could be regulated by two parameters controlling distance among states along the pathway and smoothness of the pathway. One advantage of the chain-of-states framework is that no specific reaction coordinates are necessary to generate the reaction pathway, because such information is implicitly represented by the structures along the pathway. The chain-of-states setup in a DPDS method greatly enhances the sufficient sampling in high-energy space between two end states, such as transition states. By removing the constraint on the end states of the pathway, DPDS will also sample pathways connecting minima on a PES in addition to the end points of the starting pathway. This feature makes DPDS an ideal method to directly explore transition pathway space. Three examples demonstrate the efficiency of DPDS methods in sampling the high-energy area important for reactions on the PES.

Generation of complementary sampled phase-only holograms.

PubMed

Tsang, P W M; Chow, Y T; Poon, T-C

2016-10-03

If an image is uniformly down-sampled into a sparse form and converted into a hologram, the phase component alone will be adequate to reconstruct the image. However, the appearance of the reconstructed image is degraded with numerous empty holes. In this paper, we present a low complexity and non-iterative solution to this problem. Briefly, two phase-only holograms are generated for an image, each based on a different down-sampling lattice. Subsequently, the holograms are displayed alternately at high frame rate. The reconstructed images of the 2 holograms will appear to be a single, densely sampled image with enhance visual quality.

Chemical derivatization for enhancing sensitivity during LC/ESI-MS/MS quantification of steroids in biological samples: a review.

PubMed

Higashi, Tatsuya; Ogawa, Shoujiro

2016-09-01

Sensitive and specific methods for the detection, characterization and quantification of endogenous steroids in body fluids or tissues are necessary for the diagnosis, pathological analysis and treatment of many diseases. Recently, liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS) has been widely used for these purposes due to its specificity and versatility. However, the ESI efficiency and fragmentation behavior of some steroids are poor, which lead to a low sensitivity. Chemical derivatization is one of the most effective methods to improve the detection characteristics of steroids in ESI-MS/MS. Based on this background, this article reviews the recent advances in chemical derivatization for the trace quantification of steroids in biological samples by LC/ESI-MS/MS. The derivatization in ESI-MS/MS is based on tagging a proton-affinitive or permanently charged moiety on the target steroid. Introduction/formation of a fragmentable moiety suitable for the selected reaction monitoring by the derivatization also enhances the sensitivity. The stable isotope-coded derivatization procedures for the steroid analysis are also described. Copyright © 2015 Elsevier Ltd. All rights reserved.

Novel flashlamp-based time-resolved fluorescence microscope reduces autofluorescence for 30-fold contrast enhancement in environmental samples

NASA Astrophysics Data System (ADS)

Connally, Russell; Veal, Duncan; Piper, James A.

2003-07-01

The abundance of naturally fluorescing components (autofluorophors) encountered in environmentally sourced samples can greatly hinder the detection and identification of fluorescently labeled target using fluorescence microscopy. Time-resolved fluorescence microscopy (TRFM) is a technique that reduces the effects of autofluorescence through precisely controlled time delays. Lanthanide chelates have fluorescence lifetimes many orders of magnitude greater than typical autofluorophors, and persist in their luminescence long after autofluorescence has ceased. An intense short pulse of (UV) light is used to excite fluorescence in the sample and after a short delay period the longer persisting fluorescence from the chelate is captured with an image-intensified CCD camera. The choice of pulsed excitation source for TRFM has a large impact on the price and performance of the instrument. A flashlamp with a short pulse duration was selected for our instrument because of the high spectral energy in the UV region and short pulse length. However, flash output decays with an approximate lifetime of 18μs and the TRFM requires a long-lived chelate to ensure probe fluorescence is still visible after decay of the flash plasma. We synthesized a recently reported fluorescent chelate (BHHCT) and conjugated it to a monoclonal antibody directed against the water-borne parasite Giardia lamblia. Fluorescence lifetime of the construct was determined to be 339μs +/- 14μs and provided a 45-fold enhancement of labeled Giardia over background using a gate delay of 100μs. Despite the sub-optimal decay characteristics of the light pulse, flashlamps have many advantages compared to optical chopper wheels and modulated lasers. Their low cost, lack of vibration, ease of interface and small footprint are important factors to consider in TRFM design.

Toward Scalable Boson Sampling with Photon Loss

NASA Astrophysics Data System (ADS)

Wang, Hui; Li, Wei; Jiang, Xiao; He, Y.-M.; Li, Y.-H.; Ding, X.; Chen, M.-C.; Qin, J.; Peng, C.-Z.; Schneider, C.; Kamp, M.; Zhang, W.-J.; Li, H.; You, L.-X.; Wang, Z.; Dowling, J. P.; Höfling, S.; Lu, Chao-Yang; Pan, Jian-Wei

2018-06-01

Boson sampling is a well-defined task that is strongly believed to be intractable for classical computers, but can be efficiently solved by a specific quantum simulator. However, an outstanding problem for large-scale experimental boson sampling is the scalability. Here we report an experiment on boson sampling with photon loss, and demonstrate that boson sampling with a few photons lost can increase the sampling rate. Our experiment uses a quantum-dot-micropillar single-photon source demultiplexed into up to seven input ports of a 16 ×16 mode ultralow-loss photonic circuit, and we detect three-, four- and fivefold coincidence counts. We implement and validate lossy boson sampling with one and two photons lost, and obtain sampling rates of 187, 13.6, and 0.78 kHz for five-, six-, and seven-photon boson sampling with two photons lost, which is 9.4, 13.9, and 18.0 times faster than the standard boson sampling, respectively. Our experiment shows an approach to significantly enhance the sampling rate of multiphoton boson sampling.

Toward Scalable Boson Sampling with Photon Loss.

PubMed

Wang, Hui; Li, Wei; Jiang, Xiao; He, Y-M; Li, Y-H; Ding, X; Chen, M-C; Qin, J; Peng, C-Z; Schneider, C; Kamp, M; Zhang, W-J; Li, H; You, L-X; Wang, Z; Dowling, J P; Höfling, S; Lu, Chao-Yang; Pan, Jian-Wei

2018-06-08

Boson sampling is a well-defined task that is strongly believed to be intractable for classical computers, but can be efficiently solved by a specific quantum simulator. However, an outstanding problem for large-scale experimental boson sampling is the scalability. Here we report an experiment on boson sampling with photon loss, and demonstrate that boson sampling with a few photons lost can increase the sampling rate. Our experiment uses a quantum-dot-micropillar single-photon source demultiplexed into up to seven input ports of a 16×16 mode ultralow-loss photonic circuit, and we detect three-, four- and fivefold coincidence counts. We implement and validate lossy boson sampling with one and two photons lost, and obtain sampling rates of 187, 13.6, and 0.78 kHz for five-, six-, and seven-photon boson sampling with two photons lost, which is 9.4, 13.9, and 18.0 times faster than the standard boson sampling, respectively. Our experiment shows an approach to significantly enhance the sampling rate of multiphoton boson sampling.

Sample stacking of fast-moving anions in capillary zone electrophoresis with pH-suppressed electroosmotic flow.

PubMed

Quirino, J P; Terabe, S

1999-07-30

On-line sample concentration of fast moving inorganic anions by large volume sample stacking (LVSS) and field enhanced sample injection (FESI) with a water plug under acidic conditions is presented. Detection sensitivity enhancements were around 100 and 1000-fold for LVSS and FESI, respectively. However, reproducibility and linearity of response in the LVSS approach is superior compared to the FESI approach.

Methods to enhance seismic faults and construct fault surfaces

NASA Astrophysics Data System (ADS)

Wu, Xinming; Zhu, Zhihui

2017-10-01

Faults are often apparent as reflector discontinuities in a seismic volume. Numerous types of fault attributes have been proposed to highlight fault positions from a seismic volume by measuring reflection discontinuities. These attribute volumes, however, can be sensitive to noise and stratigraphic features that are also apparent as discontinuities in a seismic volume. We propose a matched filtering method to enhance a precomputed fault attribute volume, and simultaneously estimate fault strikes and dips. In this method, a set of efficient 2D exponential filters, oriented by all possible combinations of strike and dip angles, are applied to the input attribute volume to find the maximum filtering responses at all samples in the volume. These maximum filtering responses are recorded to obtain the enhanced fault attribute volume while the corresponding strike and dip angles, that yield the maximum filtering responses, are recoded to obtain volumes of fault strikes and dips. By doing this, we assume that a fault surface is locally planar, and a 2D smoothing filter will yield a maximum response if the smoothing plane coincides with a local fault plane. With the enhanced fault attribute volume and the estimated fault strike and dip volumes, we then compute oriented fault samples on the ridges of the enhanced fault attribute volume, and each sample is oriented by the estimated fault strike and dip. Fault surfaces can be constructed by directly linking the oriented fault samples with consistent fault strikes and dips. For complicated cases with missing fault samples and noisy samples, we further propose to use a perceptual grouping method to infer fault surfaces that reasonably fit the positions and orientations of the fault samples. We apply these methods to 3D synthetic and real examples and successfully extract multiple intersecting fault surfaces and complete fault surfaces without holes.

Pieces of Other Worlds - Enhance YSS Education and Public Outreach Events with Extraterrestrial Samples

NASA Astrophysics Data System (ADS)

Allen, C.

2010-12-01

During the Year of the Solar System spacecraft will encounter two comets; orbit the asteroid Vesta, continue to explore Mars with rovers, and launch robotic explorers to the Moon and Mars. We have pieces of all these worlds in our laboratories. Extensive information about these unique materials, as well as actual lunar samples and meteorites, is available for display and education. The Johnson Space Center (JSC) curates NASA's extraterrestrial samples to support research, education, and public outreach. At the current time JSC curates five types of extraterrestrial samples: Moon rocks and soils collected by the Apollo astronauts Meteorites collected on US expeditions to Antarctica (including rocks from the Moon, Mars, and many asteroids including Vesta) “Cosmic dust” (asteroid and comet particles) collected by high-altitude aircraft Solar wind atoms collected by the Genesis spacecraft Comet and interstellar dust particles collected by the Stardust spacecraft These rocks, soils, dust particles, and atoms continue to be studied intensively by scientists around the world. Descriptions of the samples, research results, thousands of photographs, and information on how to request research samples are on the JSC Curation website: http://curator.jsc.nasa.gov/ NASA is eager for scientists and the public to have access to these exciting samples through our various loan procedures. NASA provides a limited number of Moon rock samples for either short-term or long-term displays at museums, planetariums, expositions, and professional events that are open to the public. The JSC Public Affairs Office handles requests for such display samples. Requestors should apply in writing to Mr. Louis Parker, JSC Exhibits Manager. He will advise successful applicants regarding provisions for receipt, display, and return of the samples. All loans will be preceded by a signed loan agreement executed between NASA and the requestor's organization. Email address: louis.a.parker@nasa.gov Sets

Multicast Parametric Synchronous Sampling

DTIC Science & Technology

2011-09-01

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

Sample Design, Sample Augmentation, and Estimation for Wave 2 of the NSHAP

PubMed Central

English, Ned; Pedlow, Steven; Kwok, Peter K.

2014-01-01

Objectives. The sample for the second wave (2010) of National Social Life, Health, and Aging Project (NSHAP) was designed to increase the scientific value of the Wave 1 (2005) data set by revisiting sample members 5 years after their initial interviews and augmenting this sample where possible. Method. There were 2 important innovations. First, the scope of the study was expanded by collecting data from coresident spouses or romantic partners. Second, to maximize the representativeness of the Wave 2 data, nonrespondents from Wave 1 were again approached for interview in the Wave 2 sample. Results. The overall unconditional response rate for the Wave 2 panel was 74%; the conditional response rate of Wave 1 respondents was 89%; the conditional response rate of partners was 84%; and the conversion rate for Wave 1 nonrespondents was 26%. Discussion. The inclusion of coresident partners enhanced the study by allowing the examination of how intimate, household relationships are related to health trajectories and by augmenting the size of the NSHAP sample size for this and future waves. The uncommon strategy of returning to Wave 1 nonrespondents reduced potential bias by ensuring that to the extent possible the whole of the original sample forms the basis for the field effort. NSHAP Wave 2 achieved its field objectives of consolidating the panel, recruiting their resident spouses or romantic partners, and converting a significant proportion of Wave 1 nonrespondents. PMID:25360016

Acute Oral Toxicity of Nitroguanidine in Mice

DTIC Science & Technology

1988-04-01

report, tbe iav tl at loa adhered to the "Guide for t e Care and U or Laboratory Animals," promulrat d by tbe Committee on Rev’ ion of tlte Guid for...microscopic examination. These areas did not respond t o special bacterial stains and may have been due to mouse hepa t i tis virus . Mic r oscopic...iiisfil ’iy noin«’ Iwp.ititio virus . An mal ID*! 84C003<»7 P.it.holooy Af-ci’ssion »•■ 30)17. Slide 19A! Eye

Tip-enhanced Raman spectroscopy and near-field polarization

NASA Astrophysics Data System (ADS)

Saito, Yuika; Mino, Toshihiro; Verma, Prabhat

2015-12-01

Tip-enhanced Raman spectroscopy (TERS) is a powerful tool for High-resolution Raman spectroscopy. In this method, a metal coated nano-tip acts as a plasmonic antenna to enhance the originally weak Raman scattering from a nanometric volume of a sample. The technique enables to detect Raman scattering light from nano-scale area and also enhance the light intensity with combination of near-filed light and localized surface plasmon generated at a metallized tip apex. Nowadays TERS is used to investigate various nano-scale samples, for examples, carbon nanotubes, graphenes DNA and biomaterials. As the TERS developed, there is high demand to investigate the properties of near-field light e.g. polarization properties. We have analyzed the polarization properties of near-field light in TERS and successfully realized the quantitative nano-imaging by visible light.

Do genetic and individual risk factors moderate the efficacy of motivational enhancement therapy? Drinking outcomes with an emerging adult sample

PubMed Central

Feldstein Ewing, Sarah W.; LaChance, Heather A.; Bryan, Angela; Hutchison, Kent E.

2010-01-01

Research indicates that motivational enhancement therapy (MET) helps catalyze reductions in problem drinking among emerging adults. However, moderators of this intervention remain relatively unknown. Therefore, the objectives of this study were: (1) to test whether a single session of MET increased motivation to reduce drinking and drinking outcomes; and (2) to examine whether genetic dopamine D4 receptor L (DRD4 L) and individual personality risk factors (impulsivity and novelty seeking) moderated the effects of the MET. These hypotheses were evaluated by randomly assigning a sample of emerging adult problem drinkers (n = 67) to receive a single session of MET or alcohol education. Follow-up data indicated that only individuals who were low in impulsivity, novelty seeking and/or who had the short DRD4 variable number of tandem repeats genotype evidenced differentially increased behavior change (taking steps toward reducing drinking) following the MET. PMID:19298319

Enhancement of the spectral selectivity of complex samples by measuring them in a frozen state at low temperatures in order to improve accuracy for quantitative analysis. Part II. Determination of viscosity for lube base oils using Raman spectroscopy.

PubMed

Kim, Mooeung; Chung, Hoeil

2013-03-07

The use of selectivity-enhanced Raman spectra of lube base oil (LBO) samples achieved by the spectral collection under frozen conditions at low temperatures was effective for improving accuracy for the determination of the kinematic viscosity at 40 °C (KV@40). A collection of Raman spectra from samples cooled around -160 °C provided the most accurate measurement of KV@40. Components of the LBO samples were mainly long-chain hydrocarbons with molecular structures that were deformable when these were frozen, and the different structural deformabilities of the components enhanced spectral selectivity among the samples. To study the structural variation of components according to the change of sample temperature from cryogenic to ambient condition, n-heptadecane and pristane (2,6,10,14-tetramethylpentadecane) were selected as representative components of LBO samples, and their temperature-induced spectral features as well as the corresponding spectral loadings were investigated. A two-dimensional (2D) correlation analysis was also employed to explain the origin for the improved accuracy. The asynchronous 2D correlation pattern was simplest at the optimal temperature, indicating the occurrence of distinct and selective spectral variations, which enabled the variation of KV@40 of LBO samples to be more accurately assessed.

Sensitivity and specificity enhanced enzyme-linked immunosorbent assay by rational hapten modification and heterogeneous antibody/coating antigen combinations for the detection of melamine in milk, milk powder and feed samples.

PubMed

Cao, Biyun; Yang, Hong; Song, Juan; Chang, Huafang; Li, Shuqun; Deng, Anping

2013-11-15

The adulteration of food products with melamine has led to an urgent requirement for sensitive, specific, rapid and reliable quantitative/screening methods. To enhance the sensitivity and specificity of the enzyme-linked immunosorbent assay (ELISA) for the detection of melamine in milk, milk powder and feed samples, rational hapten modification and heterogeneous antibody/coating antigen combinations were adopted. Three melamine derivatives with different length of carboxylic spacer at the end were synthesized and linked to carrier proteins for the production of immunogens and coating antigens. Monoclonal antibody against melamine was produced by hybridoma technology. Under optimal experimental conditions, the standard curves of the ELISAs for melamine were constructed in range of 0.1-100 ng mL(-1). The sensitivity was 10-300 times enhanced compared to those in the published literatures. The cross-reactivity values of the ELISAs also demonstrated the assays exhibited high specificity. Five samples were spiked with melamine at different concentrations and detected by the ELISA. The recovery rates of 72.8-123.0% and intra-assay coefficients of variation of 0.8-18.9% (n=3) were obtained. The ELISA for milk sample was confirmed by high-performance liquid chromatography with a high correlation coefficient of 0.9902 (n=6). The proposed ELISA was proven to be a feasible quantitative/screening method for melamine analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

Electron spin resonance of particulate soot samples from automobiles to help environmental studies.

PubMed

Yamanaka, C; Matsuda, T; Ikeya, M

2005-02-01

The application of electron spin resonance (ESR) was studied for diesel soot samples and suspended particulate matter (SPM) from automobile engines. Soot samples or diesel exhaust particles (DEP) were recovered at various points: in the exhaust pipe of a diesel engine, at the dust sampler of a highway tunnel (standard DEP), on the soundproofing wall alongside a heavy traffic road, and on the filters of a dust sampler for SPM. The diesel soot samples apparently showed two ESR spectra: one was a broad spectrum at g=2.1 with a line width of ca. 80-120 mT and the other was a sharp signal of a carbon radical at g=2.003 with a line width of 0.4 mT. Annealing experiments with a DEP sample at 250 degrees C revealed drastic enhancement of the sharp ESR signal, which suggested a thermal process of carbonization of remnant organics. An oximetric study by ESR showed an enhancement of the broad signal in the diesel soot sample as well as in the sharp ESR signal. Therefore, the main part of the broad ESR signal would be attributed to carbon radicals, which form a different configuration, probably closely interacting aggregates. Enhancement of the sharp ESR signal was not observed in the standard DEP sample under vacuum condition, which suggested less adsorption sites on the surface of DEP samples.

Candle Soot-Driven Performance Enhancement in Pyroelectric Energy Conversion

NASA Astrophysics Data System (ADS)

Azad, Puneet; Singh, V. P.; Vaish, Rahul

2018-05-01

We observed substantial enhancement in pyroelectric output with the help of candle soot coating on the surface of lead zirconate titanate (PZT). Candle soot of varying thicknesses was coated by directly exposing pyroelectric material to the candle flame. The open-circuit pyroelectric voltage and closed-circuit pyroelectric current were recorded while applying infrared heating across the uncoated and candle soot-coated samples for different heating and cooling cycles. In comparison to the uncoated sample, the maximum open-circuit voltage improves seven times for the candle soot-coated sample and electric current increases by eight times across a resistance of 10Å. Moreover, the harvested energy is enhanced by 50 times for candle soot-coated sample. Results indicate that candle soot coating is an effective and economic method to improve infrared sensing performance of pyroelectric materials.

Structure of health-enhancing behavior in adolescence: a latent-variable approach.

PubMed

Donovan, J E; Jessor, R; Costa, F M

1993-12-01

The structure of the interrelations among a variety of health-enhancing behaviors was examined using structural equation modeling analyses of questionnaire data from 1,280 middle school students and 2,219 high school students. The health-enhancing behaviors included seat belt use, adequate hours of sleep, attention to healthy diet, adequate exercise, low sedentary behavior, and regular toothbrushing. In the middle school sample, all of the health-enhancing behaviors correlated significantly but modestly with each other, except for sleep with toothbrushing. In the high school sample, all but three of the 15 correlations among the behaviors were significant. The results further show that a single underlying factor can account for the modest correlations among these health-enhancing behaviors in both samples. The generality of the single-factor model was also established for male, female, White, Hispanic, and Black students at each school level. These findings provide some support for the existence of health-related lifestyles in adolescence.

Hypoxanthine enhances the cured meat taste

PubMed Central

Nakamura, Yukinobu; Yoshida, Yuka; Hattori, Akihito

2016-01-01

Abstract We evaluated the enhancement of cured meat taste during maturation by sensory analysis. We focused on the heat‐stable sarcoplasmic fraction (HSSF) to identify the factors related to cured meat taste. Because the dry matter of HSSF contained more than 30% nitrogen, nitrogen compounds such as free amino acids, small peptides and adenosine triphosphate‐related compounds seemed to be the important components of HSSF. The samples cured with HSSF for 2 h exhibited the same taste profile as ones cured without HSSF for 168 h. Therefore, the changes in the amount and fractions of nitrogen compounds were examined in HSSF during incubation from 0 to 168 h. The concentration of hypoxanthine (Hx) gradually increased, while inosine‐5′‐monophosphate decreased during the incubation. The samples cured with pickles containing various concentrations of Hx were subjected to sensory analysis. The addition of Hx, in a dose‐dependent fashion, enhanced cured meat taste by maturation for 2 h. It was concluded that Hx is essential for the enhancement of cured meat taste. PMID:27169902

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

Sample-based engine noise synthesis using an enhanced pitch-synchronous overlap-and-add method.

PubMed

Jagla, Jan; Maillard, Julien; Martin, Nadine

2012-11-01

An algorithm for the real time synthesis of internal combustion engine noise is presented. Through the analysis of a recorded engine noise signal of continuously varying engine speed, a dataset of sound samples is extracted allowing the real time synthesis of the noise induced by arbitrary evolutions of engine speed. The sound samples are extracted from a recording spanning the entire engine speed range. Each sample is delimitated such as to contain the sound emitted during one cycle of the engine plus the necessary overlap to ensure smooth transitions during the synthesis. The proposed approach, an extension of the PSOLA method introduced for speech processing, takes advantage of the specific periodicity of engine noise signals to locate the extraction instants of the sound samples. During the synthesis stage, the sound samples corresponding to the target engine speed evolution are concatenated with an overlap and add algorithm. It is shown that this method produces high quality audio restitution with a low computational load. It is therefore well suited for real time applications.

Binding of Disordered Peptides to Kelch: Insights from Enhanced Sampling Simulations.

PubMed

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

2016-01-12

Keap1 protein plays an essential role in regulating cellular oxidative stress response and is a crucial binding hub for multiple proteins, several of which are intrinsically disordered proteins (IDP). Among Kelch's IDP binding partners, NRF2 and PTMA are the two most interesting cases. They share a highly similar binding motif; however, NRF2 binds to Kelch with a binding affinity of approximately 100-fold higher than that of PTMA. In this study, we perform an exhaustive sampling composed of 6 μs well-tempered metadynamics and 2 μs unbiased molecular dynamics (MD) simulations aiming at characterizing the binding mechanisms and structural properties of these two peptides. Our results agree with previous experimental observations that PTMA is remarkably more disordered than NRF2 in both the free and bound states. This explains PTMA's lower binding affinity. Our extensive sampling also provides valuable insights into the vast conformational ensembles of both NRF2 and PTMA, supports the hypothesis of coupled folding-binding, and confirms the essential role of linear motifs in IDP binding.

Rapid determination of 226Ra in environmental samples

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

Maxwell, Sherrod L.; Culligan, Brian K.

A new rapid method for the determination of {sup 228}Ra in natural water samples has been developed at the SRNL/EBL (Savannah River National Lab/ Environmental Bioassay Laboratory) that can be used for emergency response or routine samples. While gamma spectrometry can be employed with sufficient detection limits to determine {sup 228}Ra in solid samples (via {sup 228}Ac) , radiochemical methods that employ gas flow proportional counting techniques typically provide lower MDA (Minimal Detectable Activity) levels for the determination of {sup 228}Ra in water samples. Most radiochemical methods for {sup 228}Ra collect and purify {sup 228}Ra and allow for {sup 228}Acmore » daughter ingrowth for ~36 hours. In this new SRNL/EBL approach, {sup 228}Ac is collected and purified from the water sample without waiting to eliminate this delay. The sample preparation requires only about 4 hours so that {sup 228}Ra assay results on water samples can be achieved in < 6 hours. The method uses a rapid calcium carbonate precipitation enhanced with a small amount of phosphate added to enhance chemical yields (typically >90%), followed by rapid cation exchange removal of calcium. Lead, bismuth, uranium, thorium and protactinium isotopes are also removed by the cation exchange separation. {sup 228}Ac is eluted from the cation resin directly onto a DGA Resin cartridge attached to the bottom of the cation column to purify {sup 228}Ac. DGA Resin also removes lead and bismuth isotopes, along with Sr isotopes and {sup 90}Y. La is used to determine {sup 228}Ac chemical yield via ICP-MS, but {sup 133}Ba can also be used instead if ICP-MS assay is not available. Unlike some older methods, no lead or strontium holdback carriers or continual readjustment of sample pH is required.« less

Enhancement in sample collection for the detection of MDMA using a novel planar SPME (PSPME) device coupled to ion mobility spectrometry (IMS).

PubMed

Gura, Sigalit; Guerra-Diaz, Patricia; Lai, Hanh; Almirall, José R

2009-07-01

Trace detection of illicit drugs challenges the scientific community to develop improved sensitivity and selectivity in sampling and detection techniques. Ion mobility spectrometry (IMS) is one of the prominent trace detectors for illicit drugs and explosives, mostly due to its portability, high sensitivity and fast analysis. Current sampling methods for IMS rely on wiping suspected surfaces or withdrawing air through filters to collect particulates. These methods depend greatly on the particulates being bound onto surfaces or having sufficient vapour pressure to be airborne. Many of these compounds are not readily available in the headspace due to their low vapour pressure. This research presents a novel SPME device for enhanced air sampling and shows the use of optimized IMS by genetic algorithms to target volatile markers and/or odour signatures of illicit substances. The sampling method was based on unique static samplers, planar substrates coated with sol-gel polydimethyl siloxane (PDMS) nanoparticles, also known as planar solid-phase microextraction (PSPME). Due to its surface chemistry, high surface area and capacity, PSPME provides significant increases in sensitivity over conventional fibre SPME. The results show a 50-400 times increase in the detection capacity for piperonal, the odour signature of 3,4-methylenedioxymethamphetamine (MDMA). The PSPME-IMS technique was able to detect 600 ng of piperonal in a 30 s extraction from a quart-sized can containing 5 MDMA tablets, while detection using fibre SPME-IMS was not attainable. In a blind study of six cases suspected to contain varying amounts of MDMA in the tablets, PSPME-IMS successfully detected five positive cases and also produced no false positives or false negatives. One positive case had minimal amounts of MDMA resulting in a false negative response for fibre SPME-IMS.

H3 Histone Tail Conformation within the Nucleosome and the Impact of K14 Acetylation Studied Using Enhanced Sampling Simulation

PubMed Central

Ikebe, Jinzen; Sakuraba, Shun; Kono, Hidetoshi

2016-01-01

Acetylation of lysine residues in histone tails is associated with gene transcription. Because histone tails are structurally flexible and intrinsically disordered, it is difficult to experimentally determine the tail conformations and the impact of acetylation. In this work, we performed simulations to sample H3 tail conformations with and without acetylation. The results show that irrespective of the presence or absence of the acetylation, the H3 tail remains in contact with the DNA and assumes an α-helix structure in some regions. Acetylation slightly weakened the interaction between the tail and DNA and enhanced α-helix formation, resulting in a more compact tail conformation. We inferred that this compaction induces unwrapping and exposure of the linker DNA, enabling DNA-binding proteins (e.g., transcription factors) to bind to their target sequences. In addition, our simulation also showed that acetylated lysine was more often exposed to the solvent, which is consistent with the fact that acetylation functions as a post-translational modification recognition site marker. PMID:26967163

Determination of melamine in soil samples using surfactant-enhanced hollow fiber liquid phase microextraction followed by HPLC–UV using experimental design

PubMed Central

Sarafraz Yazdi, Ali; Raouf Yazdinezhad, Samaneh; Heidari, Tahereh

2014-01-01

Surfactant-enhanced hollow fiber liquid phase (SE-HF-LPME) microextraction was applied for the extraction of melamine in conjunction with high performance liquid chromatography with UV detection (HPLC–UV). Sodium dodecyl sulfate (SDS) was added firstly to the sample solution at pH 1.9 to form hydrophobic ion-pair with protonated melamine. Then the protonated melamine–dodecyl sulfate ion-pair (Mel–DS) was extracted from aqueous phase into organic phase immobilized in the pores and lumen of the hollow fiber. After extraction, the analyte-enriched 1-octanol was withdrawn into the syringe and injected into the HPLC. Preliminary, one variable at a time method was applied to select the type of extraction solvent. Then, in screening step, the other variables that may affect the extraction efficiency of the analyte were studied using a fractional factorial design. In the next step, a central composite design was applied for optimization of the significant factors having positive effects on extraction efficiency. The optimum operational conditions included: sample volume, 5 mL; surfactant concentration, 1.5 mM; pH 1.9; stirring rate, 1500 rpm and extraction time, 60 min. Using the optimum conditions, the method was analytically evaluated. The detection limit, relative standard deviation and linear range were 0.005 μg mL−1, 4.0% (3 μg mL−1, n = 5) and 0.01–8 μg mL−1, respectively. The performance of the procedure in extraction of melamine from the soil samples was good according to its relative recoveries in different spiking levels (95–109%). PMID:26644934

Compressive and Flexural Tests on Adobe Samples Reinforced with Wire Mesh

NASA Astrophysics Data System (ADS)

Jokhio, G. A.; Al-Tawil, Y. M. Y.; Syed Mohsin, S. M.; Gul, Y.; Ramli, N. I.

2018-03-01

Adobe is an economical, naturally available, and environment friendly construction material that offers excellent thermal and sound insulations as well as indoor air quality. It is important to understand and enhance the mechanical properties of this material, where a high degree of variation is reported in the literature owing to lack of research and standardization in this field. The present paper focuses first on the understanding of mechanical behaviour of adobe subjected to compressive stresses as well as flexure and then on enhancing the same with the help of steel wire mesh as reinforcement. A total of 22 samples were tested out of which, 12 cube samples were tested for compressive strength, whereas 10 beams samples were tested for modulus of rupture. Half of the samples in each category were control samples i.e. without wire mesh reinforcement, whereas the remaining half were reinforced with a single layer of wire mesh per sample. It has been found that the compressive strength of adobe increases by about 43% after adding a single layer of wire mesh reinforcement. The flexural response of adobe has also shown improvement with the addition of wire mesh reinforcement.

An enhanced cerium(IV)-rhodamine 6G chemiluminescence system using guest-host interactions in a lab-on-a-chip platform for estimating the total phenolic content in food samples.

PubMed

Al Haddabi, Buthaina; Al Lawati, Haider A J; Suliman, FakhrEldin O

2016-04-01

Two chemiluminescence-microfluidic (CL-MF) systems, e.g., Ce(IV)-rhodamine B (RB) and Ce(IV)-rhodamine 6G (R6G), for the determination of the total phenolic content in teas and some sweeteners were evaluated. The results indicated that the Ce(IV)-R6G system was more sensitive in comparison to the Ce(IV)-RB CL system. Therefore, a simple (CL-MF) method based on the CL of Ce(IV)-R6G was developed, and the sensitivity, selectivity and stability of this system were evaluated. Selected phenolic compounds (PCs), such as quercetin (QRC), catechin (CAT), rutin (RUT), gallic acid (GA), caffeic acid (CA) and syringic acid (SA), produced analytically useful chemiluminescence signals with low detection limits ranging from 0.35 nmol L(-1) for QRC to 11.31 nmol L(-1) for SA. The mixing sequence and the chip design were crucial, as the sensitivity and reproducibility could be substantially affected by these two factors. In addition, the anionic surfactant (i.e., sodium dodecyl sulfate (SDS)) can significantly enhance the CL signal intensity by as much as 300% for the QRC solution. Spectroscopic studies indicated that the enhancement was due to a strong guest-host interaction between the cationic R6G molecules and the anionic amphiphilic environment. Other parameters that could affect the CL intensities of the PCs were carefully optimized. Finally, the method was successfully applied to tea and sweetener samples. Six different tea samples exhibited total phenolic/antioxidant levels from 7.32 to 13.5 g per 100g of sample with respect to GA. Four different sweetener samples were also analyzed and exhibited total phenolic/antioxidant levels from 500.9 to 3422.9 mg kg(-1) with respect to GA. The method was selective, rapid and sensitive when used to estimate the total phenolic/antioxidant level, and the results were in good agreement with those reported for honey and tea samples. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigating enhanced thermoelectric performance of graphene-based nano-structures.

PubMed

Hossain, Md Sharafat; Huynh, Duc Hau; Jiang, Liming; Rahman, Sharmin; Nguyen, Phuong Duc; Al-Dirini, Feras; Hossain, Faruque; Bahk, Je-Hyeong; Skafidas, Efstratios

2018-03-08

Recently, it has been demonstrated that graphene nano-ribbons (GNRs) exhibit superior thermoelectric performance compared to graphene sheets. However, the underlying mechanism behind this enhancement has not been systematically investigated and significant opportunity remains for further enhancement of the thermoelectric performance of GNRs by optimizing their charge carrier concentration. In this work, we modulate the carrier concentration of graphene-based nano-structures using a gate voltage and investigate the resulting carrier-concentration-dependent thermoelectric parameters using the Boltzmann transport equations. We investigate the effect of energy dependent scattering time and the role of substrate-induced charge carrier fluctuation in optimizing the Seebeck coefficient and power factor. Our approach predicts the scattering mechanism and the extent of the charge carrier fluctuation in different samples and explains the enhancement of thermoelectric performance of GNR samples. Subsequently, we propose a route towards the enhancement of thermoelectric performance of graphene-based devices which can also be applied to other two-dimensional materials.

Organic SIMS: the influence of time on the ion yield enhancement by silver and gold deposition

NASA Astrophysics Data System (ADS)

Adriaensen, L.; Vangaever, F.; Gijbels, R.

2004-06-01

A series of organic dyes and pharmaceuticals was used to study the secondary ion yield enhancement by metal deposition. The molecules were dissolved in methanol and spincasted on silicon substrates. Subsequently, silver or gold was evaporated on the samples to produce a very thin coating. The coated samples, when measured with TOF-SIMS, showed a considerable increase in characteristic secondary ion intensity. Gold-evaporated samples appear to exhibit the highest signal enhancement. These observations apply to organic samples in general, an advantage that allows to use the technique of metal deposition on real-world samples. However, the observed signal increase does not occur at any given moment. The time between metal deposition on the sample surface and the measuring of the sample with TOF-SIMS appears to have an important influence on the enhancement of the secondary ion intensities. In consideration of these observations several experiments were carried out, in which the spincasted samples were measured at different times after sample preparation, i.e., after gold or silver was deposited on the sample surface. The results show that, depending on the sample and the metal deposited, the secondary ion signals reach their maximum at different times. Further study will be necessary to detect the mechanism responsible for the observed enhancement effect.

Associations between friends' disordered eating and muscle-enhancing behaviors

PubMed Central

Eisenberg, Marla E.; Wall, Melanie; Shim, Jin Joo; Bruening, Meg; Loth, Katie; Neumark-Sztainer, Dianne

2012-01-01

Dieting, unhealthy weight control and muscle-enhancing behaviors are common among adolescents: friends are a probable source of influence on these behaviors. The present study uses data provided by nominated friends to examine associations between friends' disordered eating and muscle-enhancing behaviors and participants' own behaviors in a diverse sample of American youth. Male and female adolescents (mean age = 14.4) completed surveys and identified their friends from a class roster; friends' survey data were then linked to each participant. Participants (N = 2126) who had at least one nominated friend were included in the analytic sample. Independent variables were created using the same weight control and muscle-enhancing behaviors reported by nominated friends, and were used in logistic regression models to test associations between participants' and their friends' behaviors, stratified by gender. Results indicated that dieting, disordered eating and muscle-enhancing behaviors were common in this sample, and selected friends' behaviors were associated with the same behaviors in participants. For example, girls whose friends reported extreme weight control behaviors had significantly greater odds of using these behaviors than girls whose friends did not report these same behaviors (OR = 2.39). This research suggests that friends' weight- and shape-related behaviors are a feature of social relationships, and is the first report demonstrating these associations for muscle-enhancing behaviors. Capitalizing on the social element may be important to the development of increasingly effective intervention and prevention programs. PMID:23010337

Signal enhancement using a switchable magnetic trap

DOEpatents

Beer, Neil Reginald [Pleasanton, CA

2012-05-29

A system for analyzing a sample including providing a microchannel flow channel; associating the sample with magnetic nanoparticles or magnetic polystyrene-coated beads; moving the sample with said magnetic nanoparticles or magnetic polystyrene-coated beads in the microchannel flow channel; holding the sample with the magnetic nanoparticles or magnetic polystyrene-coated beads in a magnetic trap in the microchannel flow channel; and analyzing the sample obtaining an enhanced analysis signal. An apparatus for analysis of a sample includes magnetic particles connected to the sample, a microchip, a flow channel in the microchip, a source of carrier fluid connected to the flow channel for moving the sample in the flow channel, an electromagnet trap connected to the flow line for selectively magnetically trapping the sample and the magnetic particles, and an analyzer for analyzing the sample.

Laser remote sensing of backscattered light from a target sample

DOEpatents

Sweatt, William C [Albuquerque, NM; Williams, John D [Albuquerque, NM

2008-02-26

A laser remote sensing apparatus comprises a laser to provide collimated excitation light at a wavelength; a sensing optic, comprising at least one optical element having a front receiving surface to focus the received excitation light onto a back surface comprising a target sample and wherein the target sample emits a return light signal that is recollimated by the front receiving surface; a telescope for collecting the recollimated return light signal from the sensing optic; and a detector for detecting and spectrally resolving the return light signal. The back surface further can comprise a substrate that absorbs the target sample from an environment. For example the substrate can be a SERS substrate comprising a roughened metal surface. The return light signal can be a surface-enhanced Raman signal or laser-induced fluorescence signal. For fluorescence applications, the return signal can be enhanced by about 10.sup.5, solely due to recollimation of the fluorescence return signal. For SERS applications, the return signal can be enhanced by 10.sup.9 or more, due both to recollimation and to structuring of the SERS substrate so that the incident laser and Raman scattered fields are in resonance with the surface plasmons of the SERS substrate.

Impact of sampling techniques on measured stormwater quality data for small streams

USDA-ARS?s Scientific Manuscript database

Science-based sampling methodologies are needed to enhance water quality characterization for developing Total Maximum Daily Loads (TMDLs), setting appropriate water quality standards, and managing nonpoint source pollution. Storm event sampling, which is vital for adequate assessment of water qual...

The "Anatomy" of a Performance-Enhancing Drug Test in Sports

ERIC Educational Resources Information Center

Werner, T. C.

2012-01-01

The components of a performance-enhancing drug (PED) test in sports include sample selection, collection, establishing sample integrity, sample pretreatment, analyte detection, data evaluation, reporting results, and action taken based on the result. Undergraduate curricula generally focus on the detection and evaluation steps of an analytical…

Tackling sampling challenges in biomolecular simulations.

PubMed

Barducci, Alessandro; Pfaendtner, Jim; Bonomi, Massimiliano

2015-01-01

Molecular dynamics (MD) simulations are a powerful tool to give an atomistic insight into the structure and dynamics of proteins. However, the time scales accessible in standard simulations, which often do not match those in which interesting biological processes occur, limit their predictive capabilities. Many advanced sampling techniques have been proposed over the years to overcome this limitation. This chapter focuses on metadynamics, a method based on the introduction of a time-dependent bias potential to accelerate sampling and recover equilibrium properties of a few descriptors that are able to capture the complexity of a process at a coarse-grained level. The theory of metadynamics and its combination with other popular sampling techniques such as the replica exchange method is briefly presented. Practical applications of these techniques to the study of the Trp-Cage miniprotein folding are also illustrated. The examples contain a guide for performing these calculations with PLUMED, a plugin to perform enhanced sampling simulations in combination with many popular MD codes.

A sampling model of social judgment.

PubMed

Galesic, Mirta; Olsson, Henrik; Rieskamp, Jörg

2018-04-01

Studies of social judgments have demonstrated a number of diverse phenomena that were so far difficult to explain within a single theoretical framework. Prominent examples are false consensus and false uniqueness, as well as self-enhancement and self-depreciation. Here we show that these seemingly complex phenomena can be a product of an interplay between basic cognitive processes and the structure of social and task environments. We propose and test a new process model of social judgment, the social sampling model (SSM), which provides a parsimonious quantitative account of different types of social judgments. In the SSM, judgments about characteristics of broader social environments are based on sampling of social instances from memory, where instances receive activation if they belong to a target reference class and have a particular characteristic. These sampling processes interact with the properties of social and task environments, including homophily, shapes of frequency distributions, and question formats. For example, in line with the model's predictions we found that whether false consensus or false uniqueness will occur depends on the level of homophily in people's social circles and on the way questions are asked. The model also explains some previously unaccounted-for patterns of self-enhancement and self-depreciation. People seem to be well informed about many characteristics of their immediate social circles, which in turn influence how they evaluate broader social environments and their position within them. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Hypoxanthine enhances the cured meat taste.

PubMed

Ichimura, Sayaka; Nakamura, Yukinobu; Yoshida, Yuka; Hattori, Akihito

2017-02-01

We evaluated the enhancement of cured meat taste during maturation by sensory analysis. We focused on the heat-stable sarcoplasmic fraction (HSSF) to identify the factors related to cured meat taste. Because the dry matter of HSSF contained more than 30% nitrogen, nitrogen compounds such as free amino acids, small peptides and adenosine triphosphate-related compounds seemed to be the important components of HSSF. The samples cured with HSSF for 2 h exhibited the same taste profile as ones cured without HSSF for 168 h. Therefore, the changes in the amount and fractions of nitrogen compounds were examined in HSSF during incubation from 0 to 168 h. The concentration of hypoxanthine (Hx) gradually increased, while inosine-5'-monophosphate decreased during the incubation. The samples cured with pickles containing various concentrations of Hx were subjected to sensory analysis. The addition of Hx, in a dose-dependent fashion, enhanced cured meat taste by maturation for 2 h. It was concluded that Hx is essential for the enhancement of cured meat taste. © 2016 The Authors. Animal Science Journal published by John Wiley & Sons Australia, Ltd on behalf of Japanese Society of Animal Science.

Muscle-enhancing behaviors among adolescent girls and boys.

PubMed

Eisenberg, Marla E; Wall, Melanie; Neumark-Sztainer, Dianne

2012-12-01

Media images of men and women have become increasingly muscular, and muscle-enhancing techniques are available to youth. Identifying populations at risk for unhealthy muscle-enhancingbehaviors is of considerable public health importance. The current study uses a large and diverse population-based sample of adolescents to examine the prevalence of muscle-enhancing behaviors and differences across demographic characteristics, weight status, and sports team involvement. Survey data from 2793 diverse adolescents (mean age = 14.4) were collected at 20 urban middle and high schools. Use of 5 muscle-enhancing behaviors was assessed (changing eating, exercising, protein powders, steroids and other muscle-enhancing substances), and a summary score reflecting use of 3 or more behaviors was created. Logistic regression was used to test for differences in each behavior across age group, race/ethnicity, socioeconomic status, BMI category, and sports team participation. Muscle-enhancing behaviors were common in this sample for both boys and girls. For example, 34.7% used protein powders or shakes and 5.9% reported steroid use. Most behaviors were significantly more common among boys. In models mutually adjusted for all covariates, grade level, Asian race, BMI category, and sports team participation were significantly associated with the use of muscle-enhancing behaviors. For example, overweight (odds ratio = 1.45) and obese (odds ratio = 1.90) girls had significantly greater odds of using protein powders or shakes than girls of average BMI. The use of muscle-enhancing behaviors is substantially higher than has been previously reported and is cause for concern. Pediatricians and other health care providers should ask their adolescent patients about muscle-enhancing behaviors.

Equilibrium cycle pin by pin transport depletion calculations with DeCART

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

Kochunas, B.; Downar, T.; Taiwo, T.

As the Advanced Fuel Cycle Initiative (AFCI) program has matured it has become more important to utilize more advanced simulation methods. The work reported here was performed as part of the AFCI fellowship program to develop and demonstrate the capability of performing high fidelity equilibrium cycle calculations. As part of the work here, a new multi-cycle analysis capability was implemented in the DeCART code which included modifying the depletion modules to perform nuclide decay calculations, implementing an assembly shuffling pattern description, and modifying iteration schemes. During the work, stability issues were uncovered with respect to converging simultaneously the neutron flux,more » isotopics, and fluid density and temperature distributions in 3-D. Relaxation factors were implemented which considerably improved the stability of the convergence. To demonstrate the capability two core designs were utilized, a reference UOX core and a CORAIL core. Full core equilibrium cycle calculations were performed on both cores and the discharge isotopics were compared. From this comparison it was noted that the improved modeling capability was not drastically different in its prediction of the discharge isotopics when compared to 2-D single assembly or 2-D core models. For fissile isotopes such as U-235, Pu-239, and Pu-241 the relative differences were 1.91%, 1.88%, and 0.59%), respectively. While this difference may not seem large it translates to mass differences on the order of tens of grams per assembly, which may be significant for the purposes of accounting of special nuclear material. (authors)« less

Enhanced amperometric detection of metronidazole in drug formulations and urine samples based on chitosan protected tetrasulfonated copper phthalocyanine thin-film modified glassy carbon electrode.

PubMed

Meenakshi, S; Pandian, K; Jayakumari, L S; Inbasekaran, S

2016-02-01

An enhanced electrocatalytic reduction of metronidazole antibiotic drug molecule using chitosan protected tetrasulfonated copper phthalocyanine (Chit/CuTsPc) thin-film modified glassy carbon electrode (GCE) has been developed. An irreversible reduction occurs at -0.47V (vs. Ag/AgCl) using Chit/CuTsPc modified GCE. A maximum peak current value is obtained at pH1 and the electrochemical reduction reaction is a diffusion controlled one. The detection limit is found to be 0.41nM from differential pulse voltammetry (DPV) method. This present investigation method is adopted for electrochemical detection of metronidazole in drug formulation and urine samples by using DPV method. Copyright © 2015 Elsevier B.V. All rights reserved.

Syntactic Enhancement and Second Language Literacy: An Experimental Study

ERIC Educational Resources Information Center

Park, Youngmin; Warschauer, Mark

2016-01-01

This experimental study examined how the reading and writing development of sixth-grade L2 students was affected by syntactic enhancement. Visual-syntactic text formatting (VSTF) technology, which visualizes syntactic structures, was used to convert a textbook to the one with syntactic enhancement. The sample (n = 282), which was drawn from a…

Surface-Enhanced Raman Scattering Surface Selection Rules for the Proteomic Liquid Biopsy in Real Samples: Efficient Detection of the Oncoprotein c-MYC.

PubMed

Pazos, Elena; Garcia-Algar, Manuel; Penas, Cristina; Nazarenus, Moritz; Torruella, Arnau; Pazos-Perez, Nicolas; Guerrini, Luca; Vázquez, M Eugenio; Garcia-Rico, Eduardo; Mascareñas, José L; Alvarez-Puebla, Ramon A

2016-11-02

Blood-based biomarkers (liquid biopsy) offer extremely valuable tools for the noninvasive diagnosis and monitoring of tumors. The protein c-MYC, a transcription factor that has been shown to be deregulated in up to 70% of human cancers, can be used as a robust proteomic signature for cancer. Herein, we developed a rapid, highly specific, and sensitive surface-enhanced Raman scattering (SERS) assay for the quantification of c-MYC in real blood samples. The sensing scheme relies on the use of specifically designed hybrid plasmonic materials and their bioderivatization with a selective peptidic receptor modified with a SERS transducer. Peptide/c-MYC recognition events translate into measurable alterations of the SERS spectra associated with a molecular reorientation of the transducer, in agreement with the surface selection rules. The efficiency of the sensor is demonstrated in cellular lines, healthy donors and a cancer patient.

Tip-enhanced Raman mapping with top-illumination AFM.

PubMed

Chan, K L Andrew; Kazarian, Sergei G

2011-04-29

Tip-enhanced Raman mapping is a powerful, emerging technique that offers rich chemical information and high spatial resolution. Currently, most of the successes in tip-enhanced Raman scattering (TERS) measurements are based on the inverted configuration where tips and laser are approaching the sample from opposite sides. This results in the limitation of measurement for transparent samples only. Several approaches have been developed to obtain tip-enhanced Raman mapping in reflection mode, many of which involve certain customisations of the system. We have demonstrated in this work that it is also possible to obtain TERS nano-images using an upright microscope (top-illumination) with a gold-coated Si atomic force microscope (AFM) cantilever without significant modification to the existing integrated AFM/Raman system. A TERS image of a single-walled carbon nanotube has been achieved with a spatial resolution of ∼ 20-50 nm, demonstrating the potential of this technique for studying non-transparent nanoscale materials.

Demographics and sexual characteristics of sex-enhancing medication users: Study of a web-based cross-sectional sample of sexually active men.

PubMed

Ahmed, Abul-Fotouh; Alshahrani, Saad; Morgan, Anthony; Gabr, Ahmed H; Abdel-Razik, Mohamed; Daoud, Abdallah

2017-12-01

To evaluate the frequency of sex-enhancing medications (S-EM) use and to investigate the demographics and sexual characteristics of the S-EM users amongst a Saudi Arabian male population. A cross-sectional sample of 1176 Saudi Arabian men was recruited using a web-based survey between 1 January and 1 April 2015. The survey included multiple open and closed questions to assess the frequency of S-EM use; and demographics, clinical, and sexual characteristics of S-EM users, as well as their perceptions of S-EM. Amongst the participants, 1008 were sexually active and included in the data analysis. Of the sexually active participants, 402 (39.9%) reported S-EM use in the form of herbal or phosphodiesterase type 5 inhibitors at some time in their lives. Comparing S-EM users with S-EM non-users, the S-EM users had a number of demographic and sexual characteristics including: higher education level, higher income, smoking, more than one sexual partner, longer sexual activity duration, higher frequency of sexual intercourse, and lower sexual satisfaction level. Most of the S-EM users (82.1%) bought S-EM without a medical prescription and 62.5% had used them recreationally. In all, 52% of respondents used S-EM to treat ED and 69% of those who used it recreationally reported enhancement of erection with S-EM usage. Demographic and sexual characteristics of S-EM users and the attitude of the users towards the S-EM were identified amongst a Saudi Arabian male population.

Modulated Raman spectroscopy for enhanced identification of bladder tumor cells in urine samples.

PubMed

Canetta, Elisabetta; Mazilu, Michael; De Luca, Anna Chiara; Carruthers, Antonia E; Dholakia, Kishan; Neilson, Sam; Sargeant, Harry; Briscoe, Tina; Herrington, C Simon; Riches, Andrew C

2011-03-01

Standard Raman spectroscopy (SRS) is a noninvasive technique that is used in the biomedical field to discriminate between normal and cancer cells. However, the presence of a strong fluorescence background detracts from the use of SRS in real-time clinical applications. Recently, we have reported a novel modulated Raman spectroscopy (MRS) technique to extract the Raman spectra from the background. In this paper, we present the first application of MRS to the identification of human urothelial cells (SV-HUC-1) and bladder cancer cells (MGH) in urine samples. These results are compared to those obtained by SRS. Classification using the principal component analysis clearly shows that MRS allows discrimination between Raman spectra of SV-HUC-1 and MGH cells with high sensitivity (98%) and specificity (95%). MRS is also used to distinguish between SV-HUC-1 and MGH cells after exposure to urine for up to 6 h. We observe a marked change in the MRS of SV-HUC-1 and MGH cells with time in urine, indicating that the conditions of sample collection will be important for the application of this methodology to clinical urine samples.

Isotope-coded ESI-enhancing derivatization reagents for differential analysis, quantification and profiling of metabolites in biological samples by LC/MS: A review.

PubMed

Higashi, Tatsuya; Ogawa, Shoujiro

2016-10-25

The analysis of the qualitative and quantitative changes of metabolites in body fluids and tissues yields valuable information for the diagnosis, pathological analysis and treatment of many diseases. Recently, liquid chromatography/electrospray ionization-(tandem) mass spectrometry [LC/ESI-MS(/MS)] has been widely used for these purposes due to the high separation capability of LC, broad coverage of ESI for various compounds and high specificity of MS(/MS). However, there are still two major problems to be solved regarding the biological sample analysis; lack of sensitivity and limited availability of stable isotope-labeled analogues (internal standards, ISs) for most metabolites. Stable isotope-coded derivatization (ICD) can be the answer for these problems. By the ICD, different isotope-coded moieties are introduced to the metabolites and one of the resulting derivatives can serve as the IS, which minimize the matrix effects. Furthermore, the derivatization can improve the ESI efficiency, fragmentation property in the MS/MS and chromatographic behavior of the metabolites, which lead to a high sensitivity and specificity in the various detection modes. Based on this background, this article reviews the recently-reported isotope-coded ESI-enhancing derivatization (ICEED) reagents, which are key components for the ICD-based LC/MS(/MS) studies, and their applications to the detection, identification, quantification and profiling of metabolites in human and animal samples. The LC/MS(/MS) using the ICEED reagents is the powerful method especially for the differential analysis (relative quantification) of metabolites in two comparative samples, simultaneous quantification of multiple metabolites whose stable isotope-labeled ISs are not available, and submetabolome profiling. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterisation of signal enhancements achieved when utilizing a photon diode in deep Raman spectroscopy of tissue

PubMed Central

Vardaki, Martha Z.; Matousek, Pavel; Stone, Nicholas

2016-01-01

We characterise the performance of a beam enhancing element (‘photon diode’) for use in deep Raman spectroscopy (DRS) of biological tissues. The optical component enhances the number of laser photons coupled into a tissue sample by returning escaping photons back into it at the illumination zone. The method is compatible with transmission Raman spectroscopy, a deep Raman spectroscopy concept, and its implementation leads to considerable enhancement of detected Raman photon rates. In the past, the enhancement concept was demonstrated with a variety of samples (pharmaceutical tablets, tissue, etc) but it was not systematically characterized with biological tissues. In this study, we investigate the enhancing properties of the photon diode in the transmission Raman geometry as a function of: a) the depth and b) the optical properties of tissue samples. Liquid tissue phantoms were employed to facilitate systematic variation of optical properties. These were chosen to mimic optical properties of human tissues, including breast and prostate. The obtained results evidence that a photon diode can enhance Raman signals of tissues by a maximum of × 2.4, although it can also decrease the signals created towards the back of samples that exhibit high scattering or absorption properties. PMID:27375932

A Comparative Study of Welded ODS Cladding materials for AFCI/GNEP Applications

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

Indrajit Charit; Megan Frary; Darryl Butt

2011-03-31

This research project involved working on the pressure resistance welding of oxide dispersion strengthened (ODS) alloys which will have a large role to play in advanced nuclear reactors. The project also demonstrated the research collaboration between four universities and one nation laboratory (Idaho National Laboratory) with participation from an industry for developing for ODS alloys. These alloys contain a high number density of very fine oxide particles that can impart high temperature strength and radiation damage resistance suitable for in-core applications in advanced reactors. The conventional fusion welding techniques tend to produce porosity-laden microstructure in the weld region and leadmore » to the agglomeration and non-uniform distribution of the neededoxide particles. That is why two solid state welding methods - pressure resistance welding (PRW) and friction stir welding (FSW) - were chosen to be evaluated in this project. The proposal is expected to support the development of Advanced Burner Reactors (ABR) under the GNEP program (now incorporated in Fuel Cycle R&D program). The outcomes of the concluded research include training of graduate and undergraduate students and get them interested in nuclear related research.« less

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

Team KuuKulgur waits to begin the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

PubMed Central

2012-01-01

Background Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural biology. While these conformations are associated with low energies in the energy surface that underlies the protein conformational space, few existing conformational search algorithms focus on explicitly sampling low-energy local minima in the protein energy surface. Methods This work proposes a novel probabilistic search framework, PLOW, that explicitly samples low-energy local minima in the protein energy surface. The framework combines algorithmic ingredients from evolutionary computation and computational structural biology to effectively explore the subspace of local minima. A greedy local search maps a conformation sampled in conformational space to a nearby local minimum. A perturbation move jumps out of a local minimum to obtain a new starting conformation for the greedy local search. The process repeats in an iterative fashion, resulting in a trajectory-based exploration of the subspace of local minima. Results and conclusions The analysis of PLOW's performance shows that, by navigating only the subspace of local minima, PLOW is able to sample conformations near a protein's native structure, either more effectively or as well as state-of-the-art methods that focus on reproducing the native structure for a protein system. Analysis of the actual subspace of local minima shows that PLOW samples this subspace more effectively that a naive sampling approach. Additional theoretical analysis reveals that the perturbation function employed by PLOW is key to its ability to sample a diverse set of low-energy conformations. This analysis also suggests directions for further research and novel applications for the proposed framework. PMID:22759582

Generalized Ensemble Sampling of Enzyme Reaction Free Energy Pathways

PubMed Central

Wu, Dongsheng; Fajer, Mikolai I.; Cao, Liaoran; Cheng, Xiaolin; Yang, Wei

2016-01-01

Free energy path sampling plays an essential role in computational understanding of chemical reactions, particularly those occurring in enzymatic environments. Among a variety of molecular dynamics simulation approaches, the generalized ensemble sampling strategy is uniquely attractive for the fact that it not only can enhance the sampling of rare chemical events but also can naturally ensure consistent exploration of environmental degrees of freedom. In this review, we plan to provide a tutorial-like tour on an emerging topic: generalized ensemble sampling of enzyme reaction free energy path. The discussion is largely focused on our own studies, particularly ones based on the metadynamics free energy sampling method and the on-the-path random walk path sampling method. We hope that this mini presentation will provide interested practitioners some meaningful guidance for future algorithm formulation and application study. PMID:27498634

Enhancement of acidic gases in biomass burning impacted air masses over Canada

NASA Technical Reports Server (NTRS)

Lefer, B. L.; Talbot, R. W.; Harriss, R. C.; Bradshaw, J. D.; Sandholm, S. T.; Olson, J. O.; Sachse, G. W.; Collins, J.; Shipham, M. A.; Blake, D. R.

1994-01-01

Biomass-burning impacted air masses sampled over central and eastern Canada during the summer of 1990 as part of ABLE 3B contained enhanced mixing ratios of gaseous HNO3, HCOOH, CH3COOH, and what appears to be (COOH)2. These aircraft-based samples were collected from a variety of fresh burning plumes and more aged haze layers from different source regions. Values of the enhancement factor, delta X/delta CO, where X represents an acidic gas, for combustion-impacted air masses sampled both near and farther away from the fires, were relatively uniform. However, comparison of carboxylic acid emission ratios measured in laboratory fires to field plume enhancement factors indicates significant in-plume production of HCOOH. Biomass-burning appears to be an important source of HNO3, HCOOH, and CH3COOH to the troposphere over subarctic Canada.

Enhancement of Retronasal Odors by Taste

PubMed Central

Nachtigal, Danielle; Hammond, Samuel; Lim, Juyun

2012-01-01

Psychophysical studies of interactions between retronasal olfaction and taste have focused most often on the enhancement of tastes by odors, which has been attributed primarily to a response bias (i.e., halo dumping). Based upon preliminary evidence that retronasal odors could also be enhanced by taste, the present study measured both forms of enhancement using appropriate response categories. In the first experiment, subjects rated taste (“sweet,” “sour,” “salty,” and “bitter”) and odor (“other”) intensity for aqueous samples of 3 tastants (sucrose, NaCl, and citric acid) and 3 odorants (vanillin, citral, and furaneol), both alone and in taste–odor mixtures. The results showed that sucrose, but not the other taste stimuli, significantly increased the perceived intensity of all 3 odors. Enhancement of tastes by odors was inconsistent and generally weaker than enhancement of odors by sucrose. A second experiment used a flavored beverage and a custard dessert to test whether the findings from the first experiment would hold for the perception of actual foods. Adding sucrose significantly enhanced the intensity of “cherry” and “vanilla” flavors, whereas adding vanillin did not significantly enhance the intensity of sweetness. It is proposed that enhancement of retronasal odors by a sweet stimulus results from an adaptive sensory mechanism that serves to increase the salience of the flavor of nutritive foods. PMID:21798851

Laser-induced enhancement of transdermal drug delivery for lidocaine through hairless mouse skin

NASA Astrophysics Data System (ADS)

Uchizono, Takeyuki; Awazu, Kunio

2006-02-01

Transdermal drug delivery system (TDDS), which is one of drug delivery system (DDS) for increasing the effectiveness of drugs, is enhanced absorption of drugs by laser irradiation. The purpose of this study is to investigate the optimum laser parameter for enhancing TDD and to examine the mechanism of TDD enhancement. In this study, hairless mouse skins (in vitro) were irradiated with Er:YAG laser, Nd:YAG laser and free electron laser (FEL), which were set up energy density of 0.5 J/cm2/pulse and exposure time of 5 second. We examined the flux (μg/cm2/h) of lidocaine (C 14H 22N IIO, FW: 234.38) through the skins using high pressure liquid chromatography (HPLC), observed cross section of the irradiated samples using light microscope, and measured electrical resistance of the surface of skins. The HPLC results demonstrated that the TDD of the irradiated samples was enhanced 200-350 times faster than it of the non-irradiated samples. It of Nd:YAG laser, however, had no enhancement. The observation of cross section and the electrical resistance of skins were found to not remove the stratum corneum (SC), completely. These results show that laser irradiations, which has the strong absorption to skins, enhance TDD dramatically with low invasive.

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

NASA Astrophysics Data System (ADS)

Awasthi, Shalini; Nair, Nisanth N.

2017-03-01

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

Methods for multiplex template sampling in digital PCR assays.

PubMed

Petriv, Oleh I; Heyries, Kevin A; VanInsberghe, Michael; Walker, David; Hansen, Carl L

2014-01-01

The efficient use of digital PCR (dPCR) for precision copy number analysis requires high concentrations of target molecules that may be difficult or impossible to obtain from clinical samples. To solve this problem we present a strategy, called Multiplex Template Sampling (MTS), that effectively increases template concentrations by detecting multiple regions of fragmented target molecules. Three alternative assay approaches are presented for implementing MTS analysis of chromosome 21, providing a 10-fold concentration enhancement while preserving assay precision.

Permeability enhancement by shock cooling

NASA Astrophysics Data System (ADS)

Griffiths, Luke; Heap, Michael; Reuschlé, Thierry; Baud, Patrick; Schmittbuhl, Jean

2015-04-01

The permeability of an efficient reservoir, e.g. a geothermal reservoir, should be sufficient to permit the circulation of fluids. Generally speaking, permeability decreases over the life cycle of the geothermal system. As a result, is usually necessary to artificially maintain and enhance the natural permeability of these systems. One of the methods of enhancement -- studied here -- is thermal stimulation (injecting cold water at low pressure). This goal of this method is to encourage new thermal cracks within the reservoir host rocks, thereby increasing reservoir permeability. To investigate the development of thermal microcracking in the laboratory we selected two granites: a fine-grained (Garibaldi Grey granite, grain size = 0.5 mm) and a course-grained granite (Lanhelin granite, grain size = 2 mm). Both granites have an initial porosity of about 1%. Our samples were heated to a range of temperatures (100-1000 °C) and were either cooled slowly (1 °C/min) or shock cooled (100 °C/s). A systematic microstructural (2D crack area density, using standard stereological techniques, and 3D BET specific surface area measurements) and rock physical property (porosity, P-wave velocity, uniaxial compressive strength, and permeability) analysis was undertaken to understand the influence of slow and shock cooling on our reservoir granites. Microstructurally, we observe that the 2D crack surface area per unit volume and the specific surface area increase as a result of thermal stressing, and, for the same maximum temperature, crack surface area is higher in the shock cooled samples. This observation is echoed by our rock physical property measurements: we see greater changes for the shock cooled samples. We can conclude that shock cooling is an extremely efficient method of generating thermal microcracks and modifying rock physical properties. Our study highlights that thermal treatments are likely to be an efficient method for the "matrix" permeability enhancement of

Surface-enhanced Raman sensor for trace chemical detection in water

NASA Astrophysics Data System (ADS)

Lee, Vincent Y.; Farquharson, Stuart; Rainey, Petrie M.

1999-11-01

Surface-enhanced Raman spectroscopy (SERS) promises to be one of the most sensitive methods for chemical detection and in recent years SERS has been used for chemical, biochemical, environmental, and physiological applications. A variety of methods using various media (electrodes, colloids, and substrates) have been successfully developed to enhance Raman signals by six orders of magnitude and more. However, SERS has not become a routine analytical technique because these methods are unable to provide quantitative measurements. This is largely due to the inability to fabricate a sampling medium that provides reversible chemical adsorption, analysis-to-analysis reproducibility, unrestricted solution requirements (reagent concentration and pH) or sample phase (liquid or solid). In an effort to overcome these restrictions, we have developed metal-doped sol-gels to provide surface-enhancement of Raman scattering.

Diazonium Salt-Based Surface-Enhanced Raman Spectroscopy Nanosensor: Detection and Quantitation of Aromatic Hydrocarbons in Water Samples

PubMed Central

Tijunelyte, Inga; Betelu, Stéphanie; Moreau, Jonathan; Ignatiadis, Ioannis; Berho, Catherine; Lidgi-Guigui, Nathalie; Guénin, Erwann; David, Catalina; Vergnole, Sébastien; Rinnert, Emmanuel; Lamy de la Chapelle, Marc

2017-01-01

Here, we present a surface-enhanced Raman spectroscopy (SERS) nanosensor for environmental pollutants detection. This study was conducted on three polycyclic aromatic hydrocarbons (PAHs): benzo[a]pyrene (BaP), fluoranthene (FL), and naphthalene (NAP). SERS substrates were chemically functionalized using 4-dodecyl benzenediazonium-tetrafluoroborate and SERS analyses were conducted to detect the pollutants alone and in mixtures. Compounds were first measured in water-methanol (9:1 volume ratio) samples. Investigation on solutions containing concentrations ranging from 10−6 g L−1 to 10−3 g L−1 provided data to plot calibration curves and to determine the performance of the sensor. The calculated limit of detection (LOD) was 0.026 mg L−1 (10−7 mol L−1) for BaP, 0.064 mg L−1 (3.2 × 10−7 mol L−1) for FL, and 3.94 mg L−1 (3.1 × 10−5 mol L−1) for NAP, respectively. The correlation between the calculated LOD values and the octanol-water partition coefficient (Kow) of the investigated PAHs suggests that the developed nanosensor is particularly suitable for detecting highly non-polar PAH compounds. Measurements conducted on a mixture of the three analytes (i) demonstrated the ability of the developed technology to detect and identify the three analytes in the mixture; (ii) provided the exact quantitation of pollutants in a mixture. Moreover, we optimized the surface regeneration step for the nanosensor. PMID:28538680

Diazonium Salt-Based Surface-Enhanced Raman Spectroscopy Nanosensor: Detection and Quantitation of Aromatic Hydrocarbons in Water Samples.

PubMed

Tijunelyte, Inga; Betelu, Stéphanie; Moreau, Jonathan; Ignatiadis, Ioannis; Berho, Catherine; Lidgi-Guigui, Nathalie; Guénin, Erwann; David, Catalina; Vergnole, Sébastien; Rinnert, Emmanuel; Lamy de la Chapelle, Marc

2017-05-24

Here, we present a surface-enhanced Raman spectroscopy (SERS) nanosensor for environmental pollutants detection. This study was conducted on three polycyclic aromatic hydrocarbons (PAHs): benzo[a]pyrene (BaP), fluoranthene (FL), and naphthalene (NAP). SERS substrates were chemically functionalized using 4-dodecyl benzenediazonium-tetrafluoroborate and SERS analyses were conducted to detect the pollutants alone and in mixtures. Compounds were first measured in water-methanol (9:1 volume ratio) samples. Investigation on solutions containing concentrations ranging from 10 -6 g L -1 to 10 -3 g L -1 provided data to plot calibration curves and to determine the performance of the sensor. The calculated limit of detection (LOD) was 0.026 mg L -1 (10 -7 mol L -1 ) for BaP, 0.064 mg L -1 (3.2 × 10 -7 mol L -1 ) for FL, and 3.94 mg L -1 (3.1 × 10 -5 mol L -1 ) for NAP, respectively. The correlation between the calculated LOD values and the octanol-water partition coefficient (K ow ) of the investigated PAHs suggests that the developed nanosensor is particularly suitable for detecting highly non-polar PAH compounds. Measurements conducted on a mixture of the three analytes (i) demonstrated the ability of the developed technology to detect and identify the three analytes in the mixture; (ii) provided the exact quantitation of pollutants in a mixture. Moreover, we optimized the surface regeneration step for the nanosensor.

Neuronal Response Gain Enhancement prior to Microsaccades.

PubMed

Chen, Chih-Yang; Ignashchenkova, Alla; Thier, Peter; Hafed, Ziad M

2015-08-17

Neuronal response gain enhancement is a classic signature of the allocation of covert visual attention without eye movements. However, microsaccades continuously occur during gaze fixation. Because these tiny eye movements are preceded by motor preparatory signals well before they are triggered, it may be the case that a corollary of such signals may cause enhancement, even without attentional cueing. In six different macaque monkeys and two different brain areas previously implicated in covert visual attention (superior colliculus and frontal eye fields), we show neuronal response gain enhancement for peripheral stimuli appearing immediately before microsaccades. This enhancement occurs both during simple fixation with behaviorally irrelevant peripheral stimuli and when the stimuli are relevant for the subsequent allocation of covert visual attention. Moreover, this enhancement occurs in both purely visual neurons and visual-motor neurons, and it is replaced by suppression for stimuli appearing immediately after microsaccades. Our results suggest that there may be an obligatory link between microsaccade occurrence and peripheral selective processing, even though microsaccades can be orders of magnitude smaller than the eccentricities of peripheral stimuli. Because microsaccades occur in a repetitive manner during fixation, and because these eye movements reset neurophysiological rhythms every time they occur, our results highlight a possible mechanism through which oculomotor events may aid periodic sampling of the visual environment for the benefit of perception, even when gaze is prevented from overtly shifting. One functional consequence of such periodic sampling could be the magnification of rhythmic fluctuations of peripheral covert visual attention. Copyright © 2015 Elsevier Ltd. All rights reserved.

ENHANCEMENT OF LEARNING ON SAMPLE SIZE CALCULATION WITH A SMARTPHONE APPLICATION: A CLUSTER-RANDOMIZED CONTROLLED TRIAL.

PubMed

Ngamjarus, Chetta; Chongsuvivatwong, Virasakdi; McNeil, Edward; Holling, Heinz

2017-01-01

Sample size determination usually is taught based on theory and is difficult to understand. Using a smartphone application to teach sample size calculation ought to be more attractive to students than using lectures only. This study compared levels of understanding of sample size calculations for research studies between participants attending a lecture only versus lecture combined with using a smartphone application to calculate sample sizes, to explore factors affecting level of post-test score after training sample size calculation, and to investigate participants’ attitude toward a sample size application. A cluster-randomized controlled trial involving a number of health institutes in Thailand was carried out from October 2014 to March 2015. A total of 673 professional participants were enrolled and randomly allocated to one of two groups, namely, 341 participants in 10 workshops to control group and 332 participants in 9 workshops to intervention group. Lectures on sample size calculation were given in the control group, while lectures using a smartphone application were supplied to the test group. Participants in the intervention group had better learning of sample size calculation (2.7 points out of maximnum 10 points, 95% CI: 24 - 2.9) than the participants in the control group (1.6 points, 95% CI: 1.4 - 1.8). Participants doing research projects had a higher post-test score than those who did not have a plan to conduct research projects (0.9 point, 95% CI: 0.5 - 1.4). The majority of the participants had a positive attitude towards the use of smartphone application for learning sample size calculation.

Measurement of Nanoplasmonic Field Enhancement with Ultrafast Photoemission.

PubMed

Rácz, Péter; Pápa, Zsuzsanna; Márton, István; Budai, Judit; Wróbel, Piotr; Stefaniuk, Tomasz; Prietl, Christine; Krenn, Joachim R; Dombi, Péter

2017-02-08

Probing nanooptical near-fields is a major challenge in plasmonics. Here, we demonstrate an experimental method utilizing ultrafast photoemission from plasmonic nanostructures that is capable of probing the maximum nanoplasmonic field enhancement in any metallic surface environment. Directly measured field enhancement values for various samples are in good agreement with detailed finite-difference time-domain simulations. These results establish ultrafast plasmonic photoelectrons as versatile probes for nanoplasmonic near-fields.

Apollo Lunar Sample Integration into Google Moon: A New Approach to Digitization

NASA Technical Reports Server (NTRS)

Dawson, Melissa D.; Todd, nancy S.; Lofgren, Gary E.

2011-01-01

The Google Moon Apollo Lunar Sample Data Integration project is part of a larger, LASER-funded 4-year lunar rock photo restoration project by NASA s Acquisition and Curation Office [1]. The objective of this project is to enhance the Apollo mission data already available on Google Moon with information about the lunar samples collected during the Apollo missions. To this end, we have combined rock sample data from various sources, including Curation databases, mission documentation and lunar sample catalogs, with newly available digital photography of rock samples to create a user-friendly, interactive tool for learning about the Apollo Moon samples

Strong surface enhanced Raman scattering from gold nanoarrays obtained by direct laser writing

NASA Astrophysics Data System (ADS)

Ivanov, V. G.; Todorov, N. D.; Petrov, L. S.; Ritacco, T.; Giocondo, M.; Vlakhov, E. S.

2016-10-01

We report for surface enhanced Raman scattering (SERS) from arrays of gold nanoparticles produced by 2-photons photo-reduction of the metallic precursor (HAuCl4) hosted in a Poly-Vinyl Alcohol (PVA) matrix, on glass substrates. Samples with the same pattern but featuring different nanoparticles size and density were obtained by varying the writing laser power and scanning speed. The Raman spectra were recorded from samples immersed in a solution of rhodamine-6G (R6G), as well as, after exposure of the samples in xylene. SERS enhancement factors of up to ∼104 were obtained for both analytes. The measurements show that the SERS enhancement is maximized on golden strips produced at higher writing laser power and lower scanning speed, where closer nanoparticles packing is obtained..

Enhanced cell adhesion on severe peened-plasma nitrided 316L stainless steel

NASA Astrophysics Data System (ADS)

Jayalakshmi, M.; Bhat, Badekai Ramachandra; Bhat, K. Udaya

2018-04-01

Plasma nitriding is an effective technique to enhance the wear resistance of austenitic stainless steels. Recently, severe surface deformation techniques are extensively used prior to nitriding to enhance diffusion kinetics. In the present study, AISI 316L austenitic stainless steel is subjected to peening-nitriding duplex treatment and biocompatibility of treated surfaces is assessed through adhesion of the fibroblast cells. Three-fold increase in the surface microhardness is observed from the un-peened sample to the peened-nitrided sample; with severe peened sample showing intermediate hardness. Similar trend is observed in the number of the fibroblast cells attached to the sample surface. Spreading of some of the fibroblast cells is observed on the sample subjected to duplex treatment; while the other two samples showed only the spindle shaped fibroblasts. Combined influence of surface nanocrystallization and presence of nitride layer is responsible for the improved biocompatibility.

Sample dimensionality: a predictor of order-disorder in component peak distribution in multidimensional separation.

PubMed

Giddings, J C

1995-05-26

While the use of multiple dimensions in separation systems can create very high peak capacities, the effectiveness of the enhanced peak capacity in resolving large numbers of components depends strongly on whether the distribution of component peaks is ordered or disordered. Peak overlap is common in disordered distributions, even with a very high peak capacity. It is therefore of great importance to understand the origin of peak order/disorder in multidimensional separations and to address the question of whether any control can be exerted over observed levels of order and disorder and thus separation efficacy. It is postulated here that the underlying difference between ordered and disordered distributions of component peaks in separation systems is related to sample complexity as measured by a newly defined parameter, the sample dimensionality s, and by the derivative dimensionality s'. It is concluded that the type and degree of order and disorder is determined by the relationship of s (or s') to the dimensionality n of the separation system employed. Thus for some relatively simple samples (defined as having small s values), increased order and a consequent enhancement of resolution can be realized by increasing n. The resolution enhancement is in addition to the normal gain in resolving power resulting from the increased peak capacity of multidimensional systems. However, for other samples (having even smaller s values), an increase in n provides no additional benefit in enhancing component separability.

Nanostar probes for tip-enhanced spectroscopy

NASA Astrophysics Data System (ADS)

Kim, Woong; Kim, Nara; Park, Joon Won; Kim, Zee Hwan

2015-12-01

To overcome the current limit of tip-enhanced spectroscopy that is based on metallic nano-probes, we developed a new scanning probe with a metallic nanostar, a nanoparticle with sharp spikes. A Au nanoparticle of 5 nm was first attached to the end of a tip through DNA-DNA hybridization and mechanical pick-up. The nanoparticle was converted to a nanostar with a core diameter of ~70 nm and spike lengths between 50 nm and 80 nm through the reduction of Au3+ with ascorbic acid in the presence of Ag+. Fabrication yields of such tips exceeded 60%, and more than 80% of such tips showed a mechanical durability sufficient for use in scanning microscopy. Effectiveness of the new probes for tip-enhanced Raman scattering (TERS) and tip-enhanced fluorescence (TEF) was confirmed. The probes exhibited the necessary enhancement for TEF, and the tip-on and tip-off ratios varied between 5 and 100. This large tip-to-tip variability may arise from the uncontrolled orientation of the apexes of the spike with respect to the sample surface, which calls for further fabrication improvement. The result overall supports a new fabrication approach for the probe that is effective for tip-enhanced spectroscopy.To overcome the current limit of tip-enhanced spectroscopy that is based on metallic nano-probes, we developed a new scanning probe with a metallic nanostar, a nanoparticle with sharp spikes. A Au nanoparticle of 5 nm was first attached to the end of a tip through DNA-DNA hybridization and mechanical pick-up. The nanoparticle was converted to a nanostar with a core diameter of ~70 nm and spike lengths between 50 nm and 80 nm through the reduction of Au3+ with ascorbic acid in the presence of Ag+. Fabrication yields of such tips exceeded 60%, and more than 80% of such tips showed a mechanical durability sufficient for use in scanning microscopy. Effectiveness of the new probes for tip-enhanced Raman scattering (TERS) and tip-enhanced fluorescence (TEF) was confirmed. The probes exhibited

Methods for Multiplex Template Sampling in Digital PCR Assays

PubMed Central

Petriv, Oleh I.; Heyries, Kevin A.; VanInsberghe, Michael; Walker, David; Hansen, Carl L.

2014-01-01

The efficient use of digital PCR (dPCR) for precision copy number analysis requires high concentrations of target molecules that may be difficult or impossible to obtain from clinical samples. To solve this problem we present a strategy, called Multiplex Template Sampling (MTS), that effectively increases template concentrations by detecting multiple regions of fragmented target molecules. Three alternative assay approaches are presented for implementing MTS analysis of chromosome 21, providing a 10-fold concentration enhancement while preserving assay precision. PMID:24854517

Ultrasonic-energy enhance the ionic liquid-based dual microextraction to preconcentrate the lead in ground and stored rain water samples as compared to conventional shaking method.

PubMed

Nizamani, Sooraj; Kazi, Tasneem G; Afridi, Hassan I

2018-01-01

An efficient preconcentration technique based on ultrasonic-assisted ionic liquid-based dual microextraction (UA-ILDµE) method has been developed to preconcentrate the lead (Pb +2 ) in ground and stored rain water. In the current proposed method, Pb +2 was complexed with a chelating agent (dithizone), whereas an ionic liquid (1-butyl-3-methylimidazolium hexafluorophosphate) was used for extraction purpose. The ultrasonic irradiation and electrical shaking system were applied to enhance the dispersion and extraction of Pb +2 complex in aqueous samples. For second phase, dual microextraction (DµE phase), the enriched Pb +2 complex in ionic liquid, extracted back into the acidic aqueous solution and finally determined by flame atomic absorption spectrometry. Some major analytical parameters that influenced the extraction efficiency of developed method, such as pH, concentration of ligand, volume of ionic liquid and samples, time of shaking in thermostatic electrical shaker and ultrasonic bath, effect of back extracting HNO 3 volume, matrix effect, centrifugation time and rate were optimized. At the sample volume of 25mL, the calculated preconcentration factor was 62.2. The limit of detection of proposed procedure for Pb +2 ions was found to be 0.54μgL -1 . The validation of developed method was performed by the analysis of certified sample of water SRM 1643e and standard addition method in a real water sample. The extraction recovery of Pb +2 was enhanced≥2% with shaking time of 80s in ultrasonic bath as compared to used thermostatic electrical shaker, where for optimum recovery up to 10min was required. The developed procedure was successfully used for the enrichment of Pb +2 in ground and stored rain water (surface water) samples of an endemic region of Pakistan. The resulted data indicated that the ground water samples were highly contaminated with Pb +2 , while some of the surface water samples were also have higher values of Pb +2 than permissible limit of

Infrared free electron laser enhanced transdermal drug delivery

NASA Astrophysics Data System (ADS)

Awazu, Kunio; Uchizono, Takeyuki; Suzuki, Sachiko; Yoshikawa, Kazushi

2005-08-01

It is necessary to control enhancement of transdermal drug delivery with non-invasive. The present study was investigated to assess the effectivity of enhancing the drug delivery by irradiating 6-μm region mid infrared free electron laser (MIR-FEL). The enhancement of transdermal drug (lidocaine) delivery of the samples (hairless mouse skin) irradiated with lasers was examined for flux (μg/cm2/h) and total penetration amount (μg/cm2) of lidocaine by High performance Liquid Chromatography (HPLC). The flux and total amount penatration date was enhanced 200-300 fold faster than the control date by the laser irradiation. FEL irradiating had the stratum corneum, and had the less thermal damage in epidermis. The effect of 6-μm region MIR-FEL has the enhancement of transdermal drug delivery without removing the stratum corneum because it has the less thermal damage. It leads to enhancement drug delivery system with non-invasive laser treatment.

Instructor Touch Enhanced College Students' Evaluations

ERIC Educational Resources Information Center

Legg, Angela M.; Wilson, Janie H.

2013-01-01

Touch between people is associated with several outcomes, including reduced stress, more positive mood, enhanced feelings of closeness, and positive behavioral change. However, the potential utility of touch rarely has been examined in a college sample, with teachers touching their students. In the present study, we used instrumental touch…

Online analysis of five organic ultraviolet filters in environmental water samples using magnetism-enhanced monolith-based in-tube solid phase microextraction coupled with high-performance liquid chromatography.

PubMed

Mei, Meng; Huang, Xiaojia

2017-11-24

Due to the endocrine disrupting properties, organic UV filters have been a great risk for humans and other organisms. Therefore, development of accurate and effective analytical methods is needed for the determination of UV filters in environmental waters. In this work, a fast, sensitive and environmentally friendly method combining magnetism-enhanced monolith-based in-tube solid phase microextraction with high-performance liquid chromatography with diode array detection (DAD) (ME-MB-IT/SPME-HPLC-DAD) for the online analysis of five organic UV filters in environmental water samples was developed. To extract UV filters effectively, an ionic liquid-based monolithic capillary column doped with magnetic nanoparticles was prepared by in-situ polymerization and used as extraction medium of online ME-MB-IT/SPME-HPLC-DAD system. Several extraction conditions including the intensity of magnetic field, sampling and desorption flow rate, volume of sample and desorption solvent, pH value and ionic strength of sample matrix were optimized thoroughly. Under the optimized conditions, the extraction efficiencies for five organic UV filters were in the range of 44.0-100%. The limits of detection (S/N=3) and limits of quantification (S/N=10) were 0.04-0.26μg/L and 0.12-0.87μg/L, respectively. The precisions indicated by relative standard deviations (RSDs) were less than 10% for both intra- and inter-day variabilities. Finally, the developed method was successfully applied to the determination of UV filters in three environmental water samples and satisfactory results were obtained. Copyright © 2017 Elsevier B.V. All rights reserved.

Contrast-enhanced 3D micro-CT of plant tissues using different impregnation techniques.

PubMed

Wang, Zi; Verboven, Pieter; Nicolai, Bart

2017-01-01

X-ray micro-CT has increasingly been used for 3D imaging of plant structures. At the micrometer resolution however, limitations in X-ray contrast often lead to datasets with poor qualitative and quantitative measures, especially within dense cell clusters of plant tissue specimens. The current study developed protocols for delivering a cesium based contrast enhancing solution to varying plant tissue specimens for the purpose of improving 3D tissue structure characterization within plant specimens, accompanied by new image processing workflows to extract the additional data generated by the contrast enhanced scans. Following passive delivery of a 10% cesium iodide contrast solution, significant increases of 85.4 and 38.0% in analyzable cell volumes were observed in pear fruit hypanthium and tomato fruit outer mesocarp samples. A significant increase of 139.6% in the number of analyzable cells was observed in the pear fruit samples along the added ability to locate and isolate better brachysclereids and vasculature in the sample volume. Furthermore, contrast enhancement resulted in significant improvement in the definition of collenchyma and parenchyma in the petiolule of tomato leaflets, from which both qualitative and quantitative data can be extracted with respect to cell measures. However, contrast enhancement was not achieved in leaf vasculature and mesophyll tissue due to fundamental limitations. Active contrast delivery to apple fruit hypanthium samples did yield a small but insignificant increase in analyzable volume and cells, but data on vasculature can now be extracted better in correspondence to the pear hypanthium samples. Contrast delivery thus improved visualization and analysis the most in dense tissue types. The cesium based contrast enhancing protocols and workflows can be utilized to obtain detailed 3D data on the internal microstructure of plant samples, and can be adapted to additional samples of interest with minimal effort. The resulting

Diagnostic potential for gold nanoparticle-based surface-enhanced Raman spectroscopy to provide colorectal cancer screening using blood serum sample

NASA Astrophysics Data System (ADS)

Lin, Duo; Feng, Shangyuan; Pan, Jianji; Chen, Yanping; Lin, Juqiang; Sun, Liqing; Chen, Rong

2011-11-01

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique that is capable of probing the biomolecular changes associated with diseased transformation. The objective of our study was to explore gold nanoparticle based SERS to obtain blood serum biochemical information for non-invasive colorectal cancer detection. SERS measurements were performed on two groups of blood serum samples: one group from patients (n = 38) with pathologically confirmed colorectal cancer and the other group from healthy volunteers (control subjects, n = 45). Tentative assignments of the Raman bands in the measured SERS spectra suggested interesting cancer specific biomolecular changes, including an increase in the relative amounts of nucleic acid, a decrease in the percentage of saccharide and proteins contents in the blood serum of colorectal cancer patients as compared to that of healthy subjects. Principal component analysis (PCA) of the measured SERS spectra separated the spectral features of the two groups into two distinct clusters with little overlaps. Linear discriminate analysis (LDA) based on the PCA generated features differentiated the nasopharyngeal cancer SERS spectra from normal SERS spectra with high sensitivity (97.4%) and specificity (100%). The results from this exploratory study demonstrated that gold nanoparticle based SERS serum analysis combined with PCA-LDA has tremendous potential for the non-invasive detection of colorectal cancers.

Diagnostic potential for gold nanoparticle-based surface-enhanced Raman spectroscopy to provide colorectal cancer screening using blood serum sample

NASA Astrophysics Data System (ADS)

Lin, Duo; Feng, Shangyuan; Pan, Jianji; Chen, Yanping; Lin, Juqiang; Sun, Liqing; Chen, Rong

2012-03-01

Surface-enhanced Raman spectroscopy (SERS) is a vibrational spectroscopic technique that is capable of probing the biomolecular changes associated with diseased transformation. The objective of our study was to explore gold nanoparticle based SERS to obtain blood serum biochemical information for non-invasive colorectal cancer detection. SERS measurements were performed on two groups of blood serum samples: one group from patients (n = 38) with pathologically confirmed colorectal cancer and the other group from healthy volunteers (control subjects, n = 45). Tentative assignments of the Raman bands in the measured SERS spectra suggested interesting cancer specific biomolecular changes, including an increase in the relative amounts of nucleic acid, a decrease in the percentage of saccharide and proteins contents in the blood serum of colorectal cancer patients as compared to that of healthy subjects. Principal component analysis (PCA) of the measured SERS spectra separated the spectral features of the two groups into two distinct clusters with little overlaps. Linear discriminate analysis (LDA) based on the PCA generated features differentiated the nasopharyngeal cancer SERS spectra from normal SERS spectra with high sensitivity (97.4%) and specificity (100%). The results from this exploratory study demonstrated that gold nanoparticle based SERS serum analysis combined with PCA-LDA has tremendous potential for the non-invasive detection of colorectal cancers.

Evaluation of Carpet Steam and Heat Cleaners as Biological Sampling Devices

DTIC Science & Technology

2016-05-01

to develop this approach into a valuable, readily available sampling capability and to evaluate its applicability for decontamination . 15. SUBJECT...Center, Research Triangle Park, NC) for their critical review of the test plan and the final report; and  Debbie Sheppard (U.S. Army Edgewood Chemical ...established to further examine and enhance the capabilities for sampling, decontaminating , and clearing biologically contaminated areas, including the

Using Lunar Sample Disks and Resources to Promote Scientific Inquiry

NASA Technical Reports Server (NTRS)

Graff, Paige; Allen, Jaclyn; Runco, Susan

2014-01-01

This poster presentation will illustrate the use of NASA Lunar Sample Disks and resources to promote scientific inquiry and address the Next Generation Science Standards. The poster will present information on the Lunar Sample Disks, housed and managed by the Astromaterials Research and Exploration Science (ARES) Directorate at the NASA Johnson Space Center. The poster will also present information on an inquiry-based planetary sample and impact cratering unit designed to introduce students in grades 4-10 to the significance of studying the rocks, soils, and surfaces of a planetary world. The unit, consisting of many hands-on activities, provides context and background information to enhance the impact of the Lunar Sample Disks.

Health-enhancing physical activity and health-related risk in a sample of north Mexican, office-based employees.

PubMed

Gilson, Nicholas David

2007-01-01

Levels of hypertension, obesity and raised total cholesterol are increasing in Mexico. Mexicans employed within sedentary occupations may be particularly at risk of developing one, or a clustering of these health-related risk factors, due to lack of participation in health enhancing physical activity (HEPA). The purpose of this study is to examine: (a) prevalence rates of hypertension, obesity and raised total cholesterol, and (b) the link between these variables and HEPA, in a sample of North Mexican, office-based employees. Methods include an assessment of systolic/diastolic blood pressure, % body fat, total cholesterol and HEPA (7-day self-report) in 47 men (33 +/- 10 years) and 43 women (28 +/- 7 years) from Monterrey, a large industrial city in the Northeast of Mexico. Values were compared against recognised health-related thresholds to determine prevalence rates of individual health-related risk factors, along with clustering of two or more risk factors. Relationships between variables were analysed using Pearson product moment correlation. The results show Men had a high prevalence of obesity (32%) and raised total cholesterol (44%), while women's rates were lower (7% and 10% respectively). More men (59%) than women (17%) demonstrated a clustering of two or more risk factors. HEPA participation was low in both men (9%) and women (16%). A significant relationship was found between men's HEPA and % body fat (r = -0.31; p < 0.05). The high levels of inactivity found in both men and women were cause for concern, suggesting the need for innovative intervention approaches, which aim to integrate physical activity into busy working lives.

Investigation of a sample of carbon-enhanced metal-poor stars observed with FORS and GMOS

NASA Astrophysics Data System (ADS)

Caffau, E.; Gallagher, A. J.; Bonifacio, P.; Spite, M.; Duffau, S.; Spite, F.; Monaco, L.; Sbordone, L.

2018-06-01

Aims: Carbon-enhanced metal-poor (CEMP) stars represent a sizeable fraction of all known metal-poor stars in the Galaxy. Their formation and composition remains a significant topic of investigation within the stellar astrophysics community. Methods: We analysed a sample of low-resolution spectra of 30 dwarf stars, obtained using the visual and near UV FOcal Reducer and low dispersion Spectrograph for the Very Large Telescope (FORS/VLT) of the European Southern Observatory (ESO) and the Gemini Multi-Object Spectrographs (GMOS) at the GEMINI telescope, to derive their metallicity and carbon abundance. Results: We derived C and Ca from all spectra, and Fe and Ba from the majority of the stars. Conclusions: We have extended the population statistics of CEMP stars and have confirmed that in general, stars with a high C abundance belonging to the high C band show a high Ba-content (CEMP-s or -r/s), while stars with a normal C abundance or that are C-rich, but belong to the low C band, are normal in Ba (CEMP-no). Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme ID 099.D-0791.Based on observations obtained at the Gemini Observatory (processed using the Gemini IRAF package), which is operated by the Association of Universities for Research in Astronomy, Inc., under a cooperative agreement with the NSF on behalf of the Gemini partnership: the National Science Foundation (United States), the National Research Council (Canada), CONICYT (Chile), Ministerio de Ciencia, Tecnología e Innovación Productiva (Argentina), and Ministério da Ciência, Tecnologia e Inovação (Brazil).Tables 1 and 2 are also available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/614/A68

New Developments of Broadband Cavity Enhanced Spectroscopic Techniques

NASA Astrophysics Data System (ADS)

Walsh, A.; Zhao, D.; Linnartz, H.; Ubachs, W.

2013-06-01

In recent years, cavity enhanced spectroscopic techniques, such as cavity ring-down spectroscopy (CRDS), cavity enhanced absorption spectroscopy (CEAS), and broadband cavity enhanced absorption spectroscopy (BBCEAS), have been widely employed as ultra-sensitive methods for the measurement of weak absorptions and in the real-time detection of trace species. In this contribution, we introduce two new cavity enhanced spectroscopic concepts: a) Optomechanical shutter modulated BBCEAS, a variant of BBCEAS capable of measuring optical absorption in pulsed systems with typically low duty cycles. In conventional BBCEAS applications, the latter substantially reduces the signal-to-noise ratio (S/N), consequently also reducing the detection sensitivity. To overcome this, we incorporate a fast optomechanical shutter as a time gate, modulating the detection scheme of BBCEAS and increasing the effective duty cycle reaches a value close to unity. This extends the applications of BBCEAS into pulsed samples and also in time-resolved studies. b) Cavity enhanced self-absorption spectroscopy (CESAS), a new spectroscopic concept capable of studying light emitting matter (plasma, flames, combustion samples) simultaneously in absorption and emission. In CESAS, a sample (plasma, flame or combustion source) is located in an optically stable cavity consisting of two high reflectivity mirrors, and here it acts both as light source and absorbing medium. A high detection sensitivity of weak absorption is reached without the need of an external light source, such as a laser or broadband lamp. The performance is illustrated by the first CESAS result on a supersonically expanding hydrocarbon plasma. We expect CESAS to become a generally applicable analytical tool for real time and in situ diagnostics. A. Walsh, D. Zhao, W. Ubachs, H. Linnartz, J. Phys. Chem. A, {dx.doi.org/10.1021/jp310392n}, in press, 2013. A. Walsh, D. Zhao, H. Linnartz Rev. Sci. Instrum. {84}(2), 021608 2013. A. Walsh, D. Zhao

Enhanced-locality fiber-optic two-photon-fluorescence live-brain interrogation

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

Fedotov, I. V.; Doronina-Amitonova, L. V.; Russian Quantum Center, ul. Novaya 100, Skolkovo, Moscow Region 1430125

2014-02-24

Two-photon excitation is shown to substantially enhance the locality of fiber-based optical interrogation of strongly scattering biotissues. In our experiments, a high-numerical-aperture, large-core-are fiber probe is used to deliver the 200-fs output of a 100-MHz mode-locked ytterbium fiber laser to samples of live mouse brain, induce two-photon fluorescence of nitrogen–vacancy centers in diamond markers in brain sample. Fiber probes with a high numerical aperture and a large core area are shown to enable locality enhancement in fiber-laser–fiber-probe two-photon brain excitation and interrogation without sacrificing the efficiency of fluorescence response collection.

Enhanced pinning in superconducting thin films with graded pinning landscapes

NASA Astrophysics Data System (ADS)

Motta, M.; Colauto, F.; Ortiz, W. A.; Fritzsche, J.; Cuppens, J.; Gillijns, W.; Moshchalkov, V. V.; Johansen, T. H.; Sanchez, A.; Silhanek, A. V.

2013-05-01

A graded distribution of antidots in superconducting a-Mo79Ge21 thin films has been investigated by magnetization and magneto-optical imaging measurements. The pinning landscape has maximum density at the sample border, decreasing linearly towards the center. Its overall performance is noticeably superior than that for a sample with uniformly distributed antidots: For high temperatures and low fields, the critical current is enhanced, whereas the region of thermomagnetic instabilities in the field-temperature diagram is significantly suppressed. These findings confirm the relevance of graded landscapes on the enhancement of pinning efficiency, as recently predicted by Misko and Nori [Phys. Rev. B 85, 184506 (2012)].

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

NASA Astrophysics Data System (ADS)

Yang, Y. Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin

2016-03-01

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling.

PubMed

Yang, Y Isaac; Zhang, Jun; Che, Xing; Yang, Lijiang; Gao, Yi Qin

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence of the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ - ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C-H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.

Efficient sampling over rough energy landscapes with high barriers: A combination of metadynamics with integrated tempering sampling

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

Yang, Y. Isaac; Zhang, Jun; Che, Xing

2016-03-07

In order to efficiently overcome high free energy barriers embedded in a complex energy landscape and calculate overall thermodynamics properties using molecular dynamics simulations, we developed and implemented a sampling strategy by combining the metadynamics with (selective) integrated tempering sampling (ITS/SITS) method. The dominant local minima on the potential energy surface (PES) are partially exalted by accumulating history-dependent potentials as in metadynamics, and the sampling over the entire PES is further enhanced by ITS/SITS. With this hybrid method, the simulated system can be rapidly driven across the dominant barrier along selected collective coordinates. Then, ITS/SITS ensures a fast convergence ofmore » the sampling over the entire PES and an efficient calculation of the overall thermodynamic properties of the simulation system. To test the accuracy and efficiency of this method, we first benchmarked this method in the calculation of ϕ − ψ distribution of alanine dipeptide in explicit solvent. We further applied it to examine the design of template molecules for aromatic meta-C—H activation in solutions and investigate solution conformations of the nonapeptide Bradykinin involving slow cis-trans isomerizations of three proline residues.« less

Animation Augmented Reality Book Model (AAR Book Model) to Enhance Teamwork

ERIC Educational Resources Information Center

Chujitarom, Wannaporn; Piriyasurawong, Pallop

2017-01-01

This study aims to synthesize an Animation Augmented Reality Book Model (AAR Book Model) to enhance teamwork and to assess the AAR Book Model to enhance teamwork. Samples are five specialists that consist of one animation specialist, two communication and information technology specialists, and two teaching model design specialists, selected by…

Reactive Monte Carlo sampling with an ab initio potential

NASA Astrophysics Data System (ADS)

Leiding, Jeff; Coe, Joshua D.

2016-05-01

We present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH3 to those of ab initio molecular dynamics (AIMD). We find that there are regions of state space for which RxMC sampling is much more efficient than AIMD due to the "rare-event" character of chemical reactions.

Determination of nicotine by surface-enhanced Raman scattering (SERS)

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

Barber, T.E.; List, M.S.; Haas, J.W. III

1994-11-01

The analytical application of surface-enhanced Raman spectroscopy (SERS) to the determination of nicotine is demonstrated. A simple spectroelectrochemical method using a copper or silver electrode as the SERS substrate has been developed, consisting of three steps: polishing a working electrode to a mirror finish; roughening the electrode in an electrolyte solution; and, finally, depositing the nicotine analyte onto the roughened electrode after immersion in a sample solution. During the reduction cycle, a large enhancement in nicotine Raman scattering is observed at the electrode surface. The intensity of the SERS signal on a silver electrode is linear with concentration from 10more » to 900 ppb, with an estimated detection limit of 7 ppb. The total analysis time per sample is approximately five minutes. This procedure has been used to analyze the extract from a cigarette side-stream smoke sample (environmental tobacco smoke); the SERS results agree well with those of conventional gas chromatographic analysis.« less

Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking.

PubMed

Higo, Junichi; Dasgupta, Bhaskar; Mashimo, Tadaaki; Kasahara, Kota; Fukunishi, Yoshifumi; Nakamura, Haruki

2015-07-30

A novel enhanced conformational sampling method, virtual-system-coupled adaptive umbrella sampling (V-AUS), was proposed to compute 300-K free-energy landscape for flexible molecular docking, where a virtual degrees of freedom was introduced to control the sampling. This degree of freedom interacts with the biomolecular system. V-AUS was applied to complex formation of two disordered amyloid-β (Aβ30-35 ) peptides in a periodic box filled by an explicit solvent. An interpeptide distance was defined as the reaction coordinate, along which sampling was enhanced. A uniform conformational distribution was obtained covering a wide interpeptide distance ranging from the bound to unbound states. The 300-K free-energy landscape was characterized by thermodynamically stable basins of antiparallel and parallel β-sheet complexes and some other complex forms. Helices were frequently observed, when the two peptides contacted loosely or fluctuated freely without interpeptide contacts. We observed that V-AUS converged to uniform distribution more effectively than conventional AUS sampling did. © 2015 Wiley Periodicals, Inc.

Analysis of IAEA Environmental Samples for Plutonium and Uranium by ICP/MS in Support Of International Safeguards

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

Farmer, Orville T.; Olsen, Khris B.; Thomas, May-Lin P.

2008-05-01

A method for the separation and determination of total and isotopic uranium and plutonium by ICP-MS was developed for IAEA samples on cellulose-based media. Preparation of the IAEA samples involved a series of redox chemistries and separations using TRU® resin (Eichrom). The sample introduction system, an APEX nebulizer (Elemental Scientific, Inc), provided enhanced nebulization for a several-fold increase in sensitivity and reduction in background. Application of mass bias (ALPHA) correction factors greatly improved the precision of the data. By combining the enhancements of chemical separation, instrumentation and data processing, detection levels for uranium and plutonium approached high attogram levels.

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

The team Survey robot retrieves a sample during a demonstration of the level two challenge at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

Sample Return Robot Challenge staff members confer before the team Survey robots makes it's attempt at the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

The team Mountaineers robot is seen after picking up the sample during a rerun of the level one challenge at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

A team KuuKulgur robot approaches the sample as it attempts the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

Sampling strategies exploiting multi-pumping flow systems.

PubMed

Prior, João A V; Santos, João L M; Lima, José L F C

2003-04-01

In this work new strategies were exploited to implement multi-pumping flow systems relying on the utilisation of multiple devices that act simultaneously as sample-insertion, reagent-introduction, and solution-propelling units. The solenoid micro-pumps that were initially used as the only active elements of multi-pumping systems, and which were able to produce pulses of 3 to 25 microL, were replaced by syringe pumps with the aim of producing pulses between 1 and 4 microL. The performance of the developed flow system was assessed by using distinct sample-insertion strategies like single sample volume, merging zones, and binary sampling in the spectrophotometric determination of isoniazid in pharmaceutical formulations upon reaction with 1,2-naphthoquinone-4-sulfonate, in alkaline medium. The results obtained showed that enhanced sample/reagent mixing could be obtained with binary sampling and by using a 1 microL per step pump, even in limited dispersion conditions. Moreover, syringe pumps produce very reproducible flowing streams and are easily manipulated and controlled by a computer program, which is greatly simplified since they are the only active manifold component. Linear calibration plots up to 18.0 microg mL(-1), with a relative standard deviation of less than 1.48% (n=10) and a throughput of about 20 samples per hour, were obtained.

Application of dispersive liquid-liquid microextraction coupled with vortex-assisted hydrophobic magnetic nanoparticles based solid-phase extraction for determination of aflatoxin M1 in milk samples by sensitive micelle enhanced spectrofluorimetry.

PubMed

Amoli-Diva, Mitra; Taherimaslak, Zohreh; Allahyari, Mehdi; Pourghazi, Kamyar; Manafi, Mohammad Hanif

2015-03-01

An efficient, simple and fast low-density solvent based dispersive liquid-liquid microextraction (LDS-DLLME) followed by vortex-assisted dispersive solid phase extraction (VA-D-SPE) has been developed as a new approach for extraction and preconcentration of aflatoxin M1 in milk samples prior to its micelle enhanced spectrofluorimetic determination. In this LDS-DLLME coupled VA-D-SPE method, milk samples were first treated with methanol/water (80:20, v/v) after removing the fat layer. This solvent was directly used as the dispersing solvent in DLLME along with using 1-heptanol (as a low-density solvent with respect to water) as the extracting solvent. In VA-D-SPE approach, hydrophobic oleic acid modified Fe3O4 nanoparticles were used to retrieve the analyte from the DLLME step. It is considerably that the target of VA-D-SPE was 1-heptanol rather than the aflatoxin M1 directly. The main parameters affecting the efficiency of LDS-DLLME and VA-D-SPE procedures and signal enhancement of aflatoxin M1 were investigated and optimized. Under the optimum conditions, the method was linear in the range from 0.02 to 200 µg L(-1) with the correlation coefficient (R(2)) of 0.9989 and detection limit of 13 ng L(-1). The intra-day precision was 2.9 and 4.3% and the inter-day precision was 2.1 and 3.3% for concentration of 2 and 50 µg L(-1) respectively. The developed method was applied for extraction and preconcentration of AFM1 in three commercially available milk samples and the results were compared with the official AOAC method. Copyright © 2014 Elsevier B.V. All rights reserved.

Tip-enhanced near-field optical microscopy

PubMed Central

Mauser, Nina; Hartschuh, Achim

2013-01-01

Tip-enhanced near-field optical microscopy (TENOM) is a scanning probe technique capable of providing a broad range of spectroscopic information on single objects and structured surfaces at nanometer spatial resolution and with highest detection sensitivity. In this review, we first illustrate the physical principle of TENOM that utilizes the antenna function of a sharp probe to efficiently couple light to excitations on nanometer length scales. We then discuss the antenna-induced enhancement of different optical sample responses including Raman scattering, fluorescence, generation of photocurrent and electroluminescence. Different experimental realizations are presented and several recent examples that demonstrate the capabilities of the technique are reviewed. PMID:24100541

Microscale surface modifications for heat transfer enhancement.

PubMed

Bostanci, Huseyin; Singh, Virendra; Kizito, John P; Rini, Daniel P; Seal, Sudipta; Chow, Louis C

2013-10-09

In this experimental study, two surface modification techniques were investigated for their effect on heat transfer enhancement. One of the methods employed the particle (grit) blasting to create microscale indentations, while the other used plasma spray coating to create microscale protrusions on Al 6061 (aluminum alloy 6061) samples. The test surfaces were characterized using scanning electron microscopy (SEM) and confocal scanning laser microscopy. Because of the surface modifications, the actual surface area was increased up to 2.8× compared to the projected base area, and the arithmetic mean roughness value (Ra) was determined to vary from 0.3 μm for the reference smooth surface to 19.5 μm for the modified surfaces. Selected samples with modified surfaces along with the reference smooth surface were then evaluated for their heat transfer performance in spray cooling tests. The cooling system had vapor-atomizing nozzles and used anhydrous ammonia as the coolant in order to achieve heat fluxes up to 500 W/cm(2) representing a thermal management setting for high power systems. Experimental results showed that the microscale surface modifications enhanced heat transfer coefficients up to 76% at 500 W/cm(2) compared to the smooth surface and demonstrated the benefits of these practical surface modification techniques to enhance two-phase heat transfer process.

Enhancing Thinking Skills in Early Childhood

ERIC Educational Resources Information Center

Aubrey, Carol; Ghent, Kathryn; Kanira, Eleni

2012-01-01

A case study approach was adopted to investigate two thinking skills programmes for a maximum variation sample of five- to six-year-olds in four schools, in two local authorities (LAs), in England and Wales, using multiple methods. School staff interviewed felt that thinking skills programmes enhanced critical thinking skills and improved use of…

Determination of 2-methoxyestradiol in serum samples and pharmaceutical preparations by silver nanoparticles-enhanced chemiluminescence.

PubMed

Zhang, Min; Xiao, Xiangqin; Zeng, Wenyuan; Zeng, Xiaoying; Yao, Hanchun

2014-03-01

Silver nanoparticles (AgNPs) exhibited better chemiluminescence (CL) catalysis activity and smaller nanoparticles have stronger catalysis ability in luminol-K3Fe(CN)6 system among the synthesized AgNPs of different size. 10±2 nm nanoparticles was used as catalysts to enhance the reaction sensitivity. It was found that the CL intensity of AgNPs-luminol-K3Fe(CN)6 was strongly inhibited in the presence of 2-methoxyestradiol (2-ME) and the relative CL intensity was in linear correlation with the concentration of 2-ME. Thus, the silver nanoparticles-enhanced CL method for the determination of 2-ME was developed. The proposed method has a detection limit (3 Sb/K) of 5.0×10(-10) mol L(-1) with a relative standard deviation of 0.75% for 5.0×10(-8) mol L(-1) 2-ME. The method was successfully applied for determination of 2-ME in human serum and pharmaceutical preparations. The possible CL reaction mechanism was also discussed briefly. Oxygen radicals played an important role in the catalytic process. Copyright © 2013 Elsevier B.V. All rights reserved.

Environmental Education Activities to Enhance Decision-Making.

ERIC Educational Resources Information Center

Yambert, Paul A.; And Others

This document contains a set of 10 activities that teachers may use with students (ages 10 to adult) to enhance environmental knowledge and environmentally responsible behavior. Sample worksheets are included when applicable. The activities focus on: renewable and nonrenewable resources; recycling; population growth; wildlife; recycling in a…

Robust sampling of decision information during perceptual choice

PubMed Central

Vandormael, Hildward; Herce Castañón, Santiago; Balaguer, Jan; Li, Vickie; Summerfield, Christopher

2017-01-01

Humans move their eyes to gather information about the visual world. However, saccadic sampling has largely been explored in paradigms that involve searching for a lone target in a cluttered array or natural scene. Here, we investigated the policy that humans use to overtly sample information in a perceptual decision task that required information from across multiple spatial locations to be combined. Participants viewed a spatial array of numbers and judged whether the average was greater or smaller than a reference value. Participants preferentially sampled items that were less diagnostic of the correct answer (“inlying” elements; that is, elements closer to the reference value). This preference to sample inlying items was linked to decisions, enhancing the tendency to give more weight to inlying elements in the final choice (“robust averaging”). These findings contrast with a large body of evidence indicating that gaze is directed preferentially to deviant information during natural scene viewing and visual search, and suggest that humans may sample information “robustly” with their eyes during perceptual decision-making. PMID:28223519

Use of complementary and alternative medicines by a sample of Turkish women for infertility enhancement: a descriptive study

PubMed Central

2010-01-01

Background Infertility patients are a vulnerable group that often seeks a non-medical solution for their failure to conceive. World-wide, women use CAM for productive health, but only a limited number of studies report on CAM use to enhance fertility. Little is known about traditional and religious forms of therapies that are used in relation to conventional medicine in Turkey. We investigated the prevalence and types of complementary and alternative medicine (CAM) used by infertile Turkish women for fertility enhancement. Methods A face-to-face questionnaire inquiring demographic information and types of CAM used for fertility enhancement were completed by hundred infertility patients admitted to a primary care family planning centre in Van, Turkey between January and July 2009. Results The vast majority of infertile women had used CAM at least once for infertility. CAM use included religious interventions, herbal products and recommendations of traditional "hodja's" (faith healers). Of these women, 87.8% were abused in the last 12 months, 36.6% felt not being supported by her partner and 80.5% had never spoken with a physician about CAM. Conclusions Infertile Turkish women use complementary medicine frequently for fertility enhancement and are in need of information about CAM. Religious and traditional therapies are used as an adjunct to, rather than a substitute for, conventional medical therapy. Physicians need to approach fertility patients with sensitivity and should be able to council their patients about CAM accordingly. PMID:20307291

Ultrasound enhanced glucose release from corn in ethanol plants.

PubMed

Khanal, Samir Kumar; Montalbo, Melissa; van Leeuwen, J; Srinivasan, Gowrishankar; Grewell, David

2007-12-01

This work evaluated the use of high power ultrasonic energy to treat corn slurry in dry corn milling ethanol plants to enhance liquefaction and saccharification for ethanol production. Corn slurry samples obtained before and after jet cooking were subjected to ultrasonic pretreatment for 20 and 40 s at amplitudes of vibration ranging from 180 to 299 microm(pp) (peak to peak amplitude in microm). The resulting samples were then exposed to enzymes (alpha-amylase and glucoamylase) to convert cornstarch into glucose. A comparison of scanning electron micrographs of raw and sonicated samples showed the development of micropores and the disruption of cell walls in corn mash. The corn particle size declined nearly 20-fold following ultrasonic treatment at high power settings. The glucose release rate from sonicated samples increased as much as threefold compared to the control group. The efficiency of ultrasound exceeded 100% in terms of energy gain from the sugar released over the ultrasonic energy supplied. Enzymatic activity was enhanced when the corn slurry was sonicated with simultaneous addition of enzymes. This finding suggests that the ultrasonic energy did not degrade or denature the enzymes during the pretreatment.

Compact OAM microscope for edge enhancement of biomedical and object samples

NASA Astrophysics Data System (ADS)

Gozali, Richard; Nguyen, Thien-An; Bendau, Ethan; Alfano, Robert R.

2017-09-01

The production of orbital angular momentum (OAM) by using a q-plate, which functions as an electrically tunable spatial frequency filter, provides a simple and efficient method of edge contrast in biological and medical sample imaging for histological evaluation of tissue, smears, and PAP smears. An instrument producing OAM, such as a q-plate, situated at the Fourier plane of a 4f lens system, similar to the use of a high-pass spatial filter, allows the passage of high spatial frequencies and enables the production of an image with highly illuminated edges contrasted against a dark background for both opaque and transparent objects. Compared with ordinary spiral phase plates and spatial light modulators, the q-plate has the added advantage of electric control and tunability.

Tumor Infiltration in Enhancing and Non-Enhancing Parts of Glioblastoma: A Correlation with Histopathology.

PubMed

Eidel, Oliver; Burth, Sina; Neumann, Jan-Oliver; Kieslich, Pascal J; Sahm, Felix; Jungk, Christine; Kickingereder, Philipp; Bickelhaupt, Sebastian; Mundiyanapurath, Sibu; Bäumer, Philipp; Wick, Wolfgang; Schlemmer, Heinz-Peter; Kiening, Karl; Unterberg, Andreas; Bendszus, Martin; Radbruch, Alexander

2017-01-01

To correlate histopathologic findings from biopsy specimens with their corresponding location within enhancing areas, non-enhancing areas and necrotic areas on contrast enhanced T1-weighted MRI scans (cT1). In 37 patients with newly diagnosed glioblastoma who underwent stereotactic biopsy, we obtained a correlation of 561 1mm3 biopsy specimens with their corresponding position on the intraoperative cT1 image at 1.5 Tesla. Biopsy points were categorized as enhancing (CE), non-enhancing (NE) or necrotic (NEC) on cT1 and tissue samples were categorized as "viable tumor cells", "blood" or "necrotic tissue (with or without cellular component)". Cell counting was done semi-automatically. NE had the highest content of tissue categorized as viable tumor cells (89% vs. 60% in CE and 30% NEC, respectively). Besides, the average cell density for NE (3764 ± 2893 cells/mm2) was comparable to CE (3506 ± 3116 cells/mm2), while NEC had a lower cell density with 2713 ± 3239 cells/mm2. If necrotic parts and bleeds were excluded, cell density in biopsies categorized as "viable tumor tissue" decreased from the center of the tumor (NEC, 5804 ± 3480 cells/mm2) to CE (4495 ± 3209 cells/mm2) and NE (4130 ± 2817 cells/mm2). The appearance of a glioblastoma on a cT1 image (circular enhancement, central necrosis, peritumoral edema) does not correspond to its diffuse histopathological composition. Cell density is elevated in both CE and NE parts. Hence, our study suggests that NE contains considerable amounts of infiltrative tumor with a high cellularity which might be considered in resection planning.

Mass enhancement versus Stoner enhancement in strongly correlated metallic perovskites: LaNiO3 and LaCuO3

NASA Astrophysics Data System (ADS)

Zhou, J.-S.; Marshall, L. G.; Goodenough, J. B.

2014-06-01

Measurements of physical properties, including transport and magnetic properties, specific heat, and thermal conductivity, have been performed on high-quality samples of LaNiO3 and LaCuO3 synthesized under high pressure. Some measurements, such as thermoelectric power and magnetic susceptibility, have been made under high pressure. The availability of a complete set of data enables a side-by-side comparison between these two narrowband systems. We have demonstrated unambiguously the mass enhancement due to electron-electron correlations in both systems relative to the recent density functional theory results. Correlations in these narrowband systems also enhance the magnetic susceptibility. Ferromagnetic spin fluctuations give rise to a strong Stoner enhancement in the magnetic susceptibility in the quarter-filled LaNiO3. Although we are able to tune the bandwidth by either chemical substitutions or by applying hydrostatic pressure on LaNiO3, the Stoner enhancement does not lead to the Stoner instability.

Australian attitudes to DNA sample banks and genetic screening.

PubMed

Williams, Carolyn

2005-11-01

An exploration via an anonymous questionnaire of Australian public attitudes towards medical genetics and sample banking revealed the overwhelming majority views these developments with thoughtful confidence. Continued public education and awareness of these issues will allow the public to make informed decisions and enhance vigilance towards the sometimes misleading coverage in the press and media.

Magnetic resonance imaging of DNP enhancements in a rotor spinning at the magic angle

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

Perras, Frederic A.; Kobayashi, Takeshi; Pruski, Marek

Simulations performed on model, static, samples have shown that the microwave power is non-uniformly distributed in the magic angle spinning (MAS) rotor when using conventional dynamic nuclear polarization (DNP) instrumentation. Here, we applied the stray-field magic angle spinning imaging (STRAFI–MAS) experiment to generate a spatial map of the DNP enhancements in a full rotor, which is spun at a low rate in a commercial DNP–MAS NMR system. Notably, we observed that the enhancement factors produced in the center of the rotor can be twice as large as those produced at the top of the rotor. Surprisingly, we observed that themore » largest enhancement factors are observed along the axis of the rotor as opposed to against its walls, which are most directly irradiated by the microwave beam. We lastly observed that the distribution of enhancement factors can be moderately improved by degassing the sample and increasing the microwave power. The inclusion of dielectric particles greatly amplifies the enhancement factors throughout the rotor. Furthermore, the STRAFI–MAS approach can provide useful guidance for optimizing the access of microwave power to the sample, and thereby lead to further increases in sensitivity of DNP–MAS NMR.« less

Magnetic resonance imaging of DNP enhancements in a rotor spinning at the magic angle

DOE PAGES

Perras, Frederic A.; Kobayashi, Takeshi; Pruski, Marek

2016-02-23

Simulations performed on model, static, samples have shown that the microwave power is non-uniformly distributed in the magic angle spinning (MAS) rotor when using conventional dynamic nuclear polarization (DNP) instrumentation. Here, we applied the stray-field magic angle spinning imaging (STRAFI–MAS) experiment to generate a spatial map of the DNP enhancements in a full rotor, which is spun at a low rate in a commercial DNP–MAS NMR system. Notably, we observed that the enhancement factors produced in the center of the rotor can be twice as large as those produced at the top of the rotor. Surprisingly, we observed that themore » largest enhancement factors are observed along the axis of the rotor as opposed to against its walls, which are most directly irradiated by the microwave beam. We lastly observed that the distribution of enhancement factors can be moderately improved by degassing the sample and increasing the microwave power. The inclusion of dielectric particles greatly amplifies the enhancement factors throughout the rotor. Furthermore, the STRAFI–MAS approach can provide useful guidance for optimizing the access of microwave power to the sample, and thereby lead to further increases in sensitivity of DNP–MAS NMR.« less

Sampling and monitoring for the mine life cycle

USGS Publications Warehouse

McLemore, Virginia T.; Smith, Kathleen S.; Russell, Carol C.

2014-01-01

Sampling and Monitoring for the Mine Life Cycle provides an overview of sampling for environmental purposes and monitoring of environmentally relevant variables at mining sites. It focuses on environmental sampling and monitoring of surface water, and also considers groundwater, process water streams, rock, soil, and other media including air and biological organisms. The handbook includes an appendix of technical summaries written by subject-matter experts that describe field measurements, collection methods, and analytical techniques and procedures relevant to environmental sampling and monitoring.The sixth of a series of handbooks on technologies for management of metal mine and metallurgical process drainage, this handbook supplements and enhances current literature and provides an awareness of the critical components and complexities involved in environmental sampling and monitoring at the mine site. It differs from most information sources by providing an approach to address all types of mining influenced water and other sampling media throughout the mine life cycle.Sampling and Monitoring for the Mine Life Cycle is organized into a main text and six appendices that are an integral part of the handbook. Sidebars and illustrations are included to provide additional detail about important concepts, to present examples and brief case studies, and to suggest resources for further information. Extensive references are included.

Role of microextraction sampling procedures in forensic toxicology.

PubMed

Barroso, Mário; Moreno, Ivo; da Fonseca, Beatriz; Queiroz, João António; Gallardo, Eugenia

2012-07-01

The last two decades have provided analysts with more sensitive technology, enabling scientists from all analytical fields to see what they were not able to see just a few years ago. This increased sensitivity has allowed drug detection at very low concentrations and testing in unconventional samples (e.g., hair, oral fluid and sweat), where despite having low analyte concentrations has also led to a reduction in sample size. Along with this reduction, and as a result of the use of excessive amounts of potentially toxic organic solvents (with the subsequent environmental pollution and costs associated with their proper disposal), there has been a growing tendency to use miniaturized sampling techniques. Those sampling procedures allow reducing organic solvent consumption to a minimum and at the same time provide a rapid, simple and cost-effective approach. In addition, it is possible to get at least some degree of automation when using these techniques, which will enhance sample throughput. Those miniaturized sample preparation techniques may be roughly categorized in solid-phase and liquid-phase microextraction, depending on the nature of the analyte. This paper reviews recently published literature on the use of microextraction sampling procedures, with a special focus on the field of forensic toxicology.

Multisite tumor sampling enhances the detection of intratumor heterogeneity at all different temporal stages of tumor evolution.

PubMed

Erramuzpe, Asier; Cortés, Jesús M; López, José I

2018-02-01

Intratumor heterogeneity (ITH) is an inherent process of tumor development that has received much attention in previous years, as it has become a major obstacle for the success of targeted therapies. ITH is also temporally unpredictable across tumor evolution, which makes its precise characterization even more problematic since detection success depends on the precise temporal snapshot at which ITH is analyzed. New and more efficient strategies for tumor sampling are needed to overcome these difficulties which currently rely entirely on the pathologist's interpretation. Recently, we showed that a new strategy, the multisite tumor sampling, works better than the routine sampling protocol for the ITH detection when the tumor time evolution was not taken into consideration. Here, we extend this work and compare the ITH detections of multisite tumor sampling and routine sampling protocols across tumor time evolution, and in particular, we provide in silico analyses of both strategies at early and late temporal stages for four different models of tumor evolution (linear, branched, neutral, and punctuated). Our results indicate that multisite tumor sampling outperforms routine protocols in detecting ITH at all different temporal stages of tumor evolution. We conclude that multisite tumor sampling is more advantageous than routine protocols in detecting intratumor heterogeneity.

Frequency analysis for modulation-enhanced powder diffraction.

PubMed

Chernyshov, Dmitry; Dyadkin, Vadim; van Beek, Wouter; Urakawa, Atsushi

2016-07-01

Periodic modulation of external conditions on a crystalline sample with a consequent analysis of periodic diffraction response has been recently proposed as a tool to enhance experimental sensitivity for minor structural changes. Here the intensity distributions for both a linear and nonlinear structural response induced by a symmetric and periodic stimulus are analysed. The analysis is further extended for powder diffraction when an external perturbation changes not only the intensity of Bragg lines but also their positions. The derived results should serve as a basis for a quantitative modelling of modulation-enhanced diffraction data measured in real conditions.

Reactive Monte Carlo sampling with an ab initio potential

DOE PAGES

Leiding, Jeff; Coe, Joshua D.

2016-05-04

Here, we present the first application of reactive Monte Carlo in a first-principles context. The algorithm samples in a modified NVT ensemble in which the volume, temperature, and total number of atoms of a given type are held fixed, but molecular composition is allowed to evolve through stochastic variation of chemical connectivity. We also discuss general features of the method, as well as techniques needed to enhance the efficiency of Boltzmann sampling. Finally, we compare the results of simulation of NH 3 to those of ab initio molecular dynamics (AIMD). Furthermore, we find that there are regions of state spacemore » for which RxMC sampling is much more efficient than AIMD due to the “rare-event” character of chemical reactions.« less

Microcavity Enhanced Raman Scattering

NASA Astrophysics Data System (ADS)

Petrak, Benjamin J.

Raman scattering can accurately identify molecules by their intrinsic vibrational frequencies, but its notoriously weak scattering efficiency for gases presents a major obstacle to its practical application in gas sensing and analysis. This work explores the use of high finesse (≈50 000) Fabry-Perot microcavities as a means to enhance Raman scattering from gases. A recently demonstrated laser ablation method, which carves out a micromirror template on fused silica--either on a fiber tip or bulk substrates-- was implemented, characterized, and optimized to fabricate concave micromirror templates ˜10 mum diameter and radius of curvature. The fabricated templates were coated with a high-reflectivity dielectric coating by ion-beam sputtering and were assembled into microcavities ˜10 mum long and with a mode volume ˜100 mum 3. A novel gas sensing technique that we refer to as Purcell enhanced Raman scattering (PERS) was demonstrated using the assembled microcavities. PERS works by enhancing the pump laser's intensity through resonant recirculation at one longitudinal mode, while simultaneously, at a second mode at the Stokes frequency, the Purcell effect increases the rate of spontaneous Raman scattering by a change to the intra-cavity photon density of states. PERS was shown to enhance the rate of spontaneous Raman scattering by a factor of 107 compared to the same volume of sample gas in free space scattered into the same solid angle subtended by the cavity. PERS was also shown capable of resolving several Raman bands from different isotopes of CO2 gas for application to isotopic analysis. Finally, the use of the microcavity to enhance coherent anti-Stokes Raman scattering (CARS) from CO2 gas was demonstrated.

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

A sample can be seen on the competition field as the team Survey robot conducts a demonstration of the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

Phylogenomic analysis of ants, bees and stinging wasps: Improved taxon sampling enhances understanding of hymenopteran evolution

USDA-ARS?s Scientific Manuscript database

The importance of taxon sampling in phylogenetic accuracy is a topic of active debate. We investigated the role of taxon sampling in causing incongruent results between two recent phylogenomic studies of stinging wasps (Hymenoptera: Aculeata), a diverse lineage that includes ants, bees and the major...

Analytical applications of enhanced drug luminescence.

PubMed

Baeyens, W R; Ling, B L

1989-01-01

Luminescence emission from drugs is strongly dependent on their physicochemical environment. Several biomedically and environmentally important compounds and pharmaceuticals exhibit sufficient intrinsic luminescence properties to allow their determination by high-performance liquid chromatography (HPLC) with fluorimetric, chemiluminescence or room temperature phosphorimetric detection. In the case of weakly fluorescing compounds it is possible to use the dependence of the emitted radiation on the molecular environment at the moment of measurement. The composition of the eluent, i.e. solvents, added salts and buffers, pH and ionic strength, oxygen content and temperature, are of the highest importance for the luminescence detection of drugs in solution (e.g. in liquid chromatography) or adsorbed onto solid surfaces (e.g. in thin-layer chromatography). Post-column or post-plate acid-base manipulation and the use of specific reagents may remarkably enhance the observed luminescence of several molecules. The term "enhancement" of luminescence comprises various sample treatments leading to an increase of the emitted radiation. These treatments include the addition of non-fluorescent compounds to, or the creation of organized media (surfactants, cyclodextrins, heavy atoms) in, the sample to be measured. They may also involve changes in molecular environment, pH, the application of excessive drying conditions, the removal of oxygen, the protection of adsorbed compounds against non-radiative decay mechanisms by means of specific spraying or dipping conditions, amongst others. The use of organized media in luminescence spectroscopy is growing. Many of the recent studies have involved micelles for enhancing the fluorescence, room temperature phosphorescence and chemiluminescence of several chemicals. Cyclodextrins are increasingly used for various analytical applications. Liquid paraffin, triethanolamine, dodecane, Triton X-100 and Fomblin Y-Vac are commonly used

Comparison of time-gated surface-enhanced Raman spectroscopy (TG-SERS) and classical SERS based monitoring of Escherichia coli cultivation samples.

PubMed

Kögler, Martin; Paul, Andrea; Anane, Emmanuel; Birkholz, Mario; Bunker, Alex; Viitala, Tapani; Maiwald, Michael; Junne, Stefan; Neubauer, Peter

2018-06-08

The application of Raman spectroscopy as a monitoring technique for bioprocesses is severely limited by a large background signal originating from fluorescing compounds in the culture media. Here we compare time-gated Raman (TG-Raman)-, continuous wave NIR-process Raman (NIR-Raman) and continuous wave micro-Raman (micro-Raman) approaches in combination with surface enhanced Raman spectroscopy (SERS) for their potential to overcome this limit. For that purpose, we monitored metabolite concentrations of Escherichia coli bioreactor cultivations in cell-free supernatant samples. We investigated concentration transients of glucose, acetate, AMP and cAMP at alternating substrate availability, from deficiency to excess. Raman and SERS signals were compared to off-line metabolite analysis of carbohydrates, carboxylic acids and nucleotides. Results demonstrate that SERS, in almost all cases, led to a higher number of identifiable signals and better resolved spectra. Spectra derived from the TG-Raman were comparable to those of micro-Raman resulting in well-discernable Raman peaks, which allowed for the identification of a higher number of compounds. In contrast, NIR-Raman provided a superior performance for the quantitative evaluation of analytes, both with and without SERS nanoparticles when using multivariate data analysis. This article is protected by copyright. All rights reserved. © 2018 American Institute of Chemical Engineers.

Application of enhanced gas chromatography/triple quadrupole mass spectrometry for monitoring petroleum weathering and forensic source fingerprinting in samples impacted by the Deepwater Horizon oil spill.

PubMed

Adhikari, Puspa L; Wong, Roberto L; Overton, Edward B

2017-10-01

Accurate characterization of petroleum hydrocarbons in complex and weathered oil residues is analytically challenging. This is primarily due to chemical compositional complexity of both the oil residues and environmental matrices, and the lack of instrumental selectivity due to co-elution of interferences with the target analytes. To overcome these analytical selectivity issues, we used an enhanced resolution gas chromatography coupled with triple quadrupole mass spectrometry in Multiple Reaction Monitoring (MRM) mode (GC/MS/MS-MRM) to eliminate interferences within the ion chromatograms of target analytes found in environmental samples. This new GC/MS/MS-MRM method was developed and used for forensic fingerprinting of deep-water and marsh sediment samples containing oily residues from the Deepwater Horizon oil spill. The results showed that the GC/MS/MS-MRM method increases selectivity, eliminates interferences, and provides more accurate quantitation and characterization of trace levels of alkyl-PAHs and biomarker compounds, from weathered oil residues in complex sample matrices. The higher selectivity of the new method, even at low detection limits, provides greater insights on isomer and homolog compositional patterns and the extent of oil weathering under various environmental conditions. The method also provides flat chromatographic baselines for accurate and unambiguous calculation of petroleum forensic biomarker compound ratios. Thus, this GC/MS/MS-MRM method can be a reliable analytical strategy for more accurate and selective trace level analyses in petroleum forensic studies, and for tacking continuous weathering of oil residues. Copyright © 2017 Elsevier Ltd. All rights reserved.

High-throughput automated microfluidic sample preparation for accurate microbial genomics

PubMed Central

Kim, Soohong; De Jonghe, Joachim; Kulesa, Anthony B.; Feldman, David; Vatanen, Tommi; Bhattacharyya, Roby P.; Berdy, Brittany; Gomez, James; Nolan, Jill; Epstein, Slava; Blainey, Paul C.

2017-01-01

Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps. By reducing the sample quantity requirements, we enabled low-input (∼10,000 cells) whole-genome shotgun (WGS) sequencing of Mycobacterium tuberculosis and soil micro-colonies with superior results. We also leveraged the enhanced throughput to sequence ∼400 clinical Pseudomonas aeruginosa libraries and demonstrate excellent single-nucleotide polymorphism detection performance that explained phenotypically observed antibiotic resistance. Fully-integrated lab-on-chip sample preparation overcomes technical barriers to enable broader deployment of genomics across many basic research and translational applications. PMID:28128213

Focused conformational sampling in proteins

NASA Astrophysics Data System (ADS)

Bacci, Marco; Langini, Cassiano; Vymětal, Jiří; Caflisch, Amedeo; Vitalis, Andreas

2017-11-01

A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.

Scale-up of an ultrasound-enhanced bioscouring process

USDA-ARS?s Scientific Manuscript database

Using previously determined optimized reaction conditions, an ultrasound-enhanced bioscouring process was scaled to ten gallon capacity and a system of rollers was added which allowed for continuous fabric feed and equipment operation. UV-Vis photospectroscopic data from bioscoured fabric samples co...

Enhanced Resolution of Chiral Amino Acids with Capillary Electrophoresis for Biosignature Detection in Extraterrestrial Samples.

PubMed

Creamer, Jessica S; Mora, Maria F; Willis, Peter A

2017-01-17

Amino acids are fundamental building blocks of terrestrial life as well as ubiquitous byproducts of abiotic reactions. In order to distinguish between amino acids formed by abiotic versus biotic processes it is possible to use chemical distributions to identify patterns unique to life. This article describes two capillary electrophoresis methods capable of resolving 17 amino acids found in high abundance in both biotic and abiotic samples (seven enantiomer pairs d/l-Ala, -Asp, -Glu, -His, -Leu, -Ser, -Val and the three achiral amino acids Gly, β-Ala, and GABA). To resolve the 13 neutral amino acids one method utilizes a background electrolyte containing γ-cyclodextrin and sodium taurocholate micelles. The acidic amino acid enantiomers were resolved with γ-cyclodextrin alone. These methods allow detection limits down to 5 nM for the neutral amino acids and 500 nM for acidic amino acids and were used to analyze samples collected from Mono Lake with minimal sample preparation.

Rapid bacterial diagnostics via surface enhanced Raman microscopy.

PubMed

Premasiri, W R; Sauer-Budge, A F; Lee, J C; Klapperich, C M; Ziegler, L D

2012-06-01

There is a continuing need to develop new techniques for the rapid and specific identification of bacterial pathogens in human body fluids especially given the increasing prevalence of drug resistant strains. Efforts to develop a surface enhanced Raman spectroscopy (SERS) based approach, which encompasses sample preparation, SERS substrates, portable Raman microscopy instrumentation and novel identification software, are described. The progress made in each of these areas in our laboratory is summarized and illustrated by a spiked infectious sample for urinary tract infection (UTI) diagnostics. SERS bacterial spectra exhibit both enhanced sensitivity and specificity allowing the development of an easy to use, portable, optical platform for pathogen detection and identification. SERS of bacterial cells is shown to offer not only reproducible molecular spectroscopic signatures for analytical applications in clinical diagnostics, but also is a new tool for studying biochemical activity in real time at the outer layers of these organisms.

Surface-Enhanced Impulsive Coherent Vibrational Spectroscopy

PubMed Central

Du, Juan; Harra, Juha; Virkki, Matti; Mäkelä, Jyrki M.; Leng, Yuxin; Kauranen, Martti; Kobayashi, Takayoshi

2016-01-01

Surface-enhanced Raman spectroscopy (SERS) has attracted a lot of attention in molecular sensing because of the remarkable ability of plasmonic metal nanostructures to enhance the weak Raman scattering process. On the other hand, coherent vibrational spectroscopy triggered by impulsive excitation using ultrafast laser pulses provides complete information about the temporal evolution of molecular vibrations, allowing dynamical processes in molecular systems to be followed in “real time”. Here, we combine these two concepts and demonstrate surface-enhanced impulsive vibrational spectroscopy. The vibrational modes of the ground and excited states of poly[2-methoxy-5-(2-ethylhexyloxy)−1,4-phenylenevinylene] (MEH-PPV), spin-coated on a substrate covered with monodisperse silver nanoparticles, are impulsively excited with a sub-10 fs pump pulse and characterized with a delayed broad-band probe pulse. The maximum enhancement in the spectrally and temporally resolved vibrational signatures averaged over the whole sample is about 4.6, while the real-time information about the instantaneous vibrational amplitude together with the initial vibrational phase is preserved. The phase is essential to determine the vibrational contributions from the ground and excited states. PMID:27812020

Lateral Coherence and Mixing in the Coastal Ocean: Adaptive Sampling using Gliders

DTIC Science & Technology

2012-09-30

Adaptive Sampling using Gliders R. Kipp Shearman Jonathan D. Nash James N. Moum John A. Barth College of Oceanic & Atmospheric Sciences Oregon State...persistent on O (3 day) timescales, so are ideally suited to be adaptively sampled by autonomous gliders that actively report both turbulent and...plan to deploy 4 AUV gliders to perform intensive, adaptive surveys. Newly-enhanced to measure turbulent mixing, water-column currents and dye

Lateral Coherence and Mixing in the Coastal Ocean: Adaptive Sampling using Gliders

DTIC Science & Technology

2011-09-30

Coherence and Mixing in the Coastal Ocean: Adaptive Sampling using Gliders R. Kipp Shearman Jonathan D. Nash James N. Moum John A. Barth College of...These structures evolve yet are often persistent on O (3 day) timescales, so are ideally suited to be adaptively sampled by autonomous gliders that...processes driving lateral dispersion, we plan to deploy 4 AUV gliders to perform intensive, adaptive surveys. Newly-enhanced to measure turbulent mixing

Enhanced stochastic fluctuations to measure steep adhesive energy landscapes

PubMed Central

Haider, Ahmad; Potter, Daniel; Sulchek, Todd A.

2016-01-01

Free-energy landscapes govern the behavior of all interactions in the presence of thermal fluctuations in the fields of physical chemistry, materials sciences, and the biological sciences. From the energy landscape, critical information about an interaction, such as the reaction kinetic rates, bond lifetimes, and the presence of intermediate states, can be determined. Despite the importance of energy landscapes to understanding reaction mechanisms, most experiments do not directly measure energy landscapes, particularly for interactions with steep force gradients that lead to premature jump to contact of the probe and insufficient sampling of transition regions. Here we present an atomic force microscopy (AFM) approach for measuring energy landscapes that increases sampling of strongly adhesive interactions by using white-noise excitation to enhance the cantilever’s thermal fluctuations. The enhanced fluctuations enable the recording of subtle deviations from a harmonic potential to accurately reconstruct interfacial energy landscapes with steep gradients. Comparing the measured energy landscape with adhesive force measurements reveals the existence of an optimal excitation voltage that enables the cantilever fluctuations to fully sample the shape and depth of the energy surface. PMID:27911778

Spectral gap optimization of order parameters for sampling complex molecular systems

PubMed Central

Tiwary, Pratyush; Berne, B. J.

2016-01-01

In modern-day simulations of many-body systems, much of the computational complexity is shifted to the identification of slowly changing molecular order parameters called collective variables (CVs) or reaction coordinates. A vast array of enhanced-sampling methods are based on the identification and biasing of these low-dimensional order parameters, whose fluctuations are important in driving rare events of interest. Here, we describe a new algorithm for finding optimal low-dimensional CVs for use in enhanced-sampling biasing methods like umbrella sampling, metadynamics, and related methods, when limited prior static and dynamic information is known about the system, and a much larger set of candidate CVs is specified. The algorithm involves estimating the best combination of these candidate CVs, as quantified by a maximum path entropy estimate of the spectral gap for dynamics viewed as a function of that CV. The algorithm is called spectral gap optimization of order parameters (SGOOP). Through multiple practical examples, we show how this postprocessing procedure can lead to optimization of CV and several orders of magnitude improvement in the convergence of the free energy calculated through metadynamics, essentially giving the ability to extract useful information even from unsuccessful metadynamics runs. PMID:26929365

An atlas of active enhancers across human cell types and tissues

NASA Astrophysics Data System (ADS)

Andersson, Robin; Gebhard, Claudia; Miguel-Escalada, Irene; Hoof, Ilka; Bornholdt, Jette; Boyd, Mette; Chen, Yun; Zhao, Xiaobei; Schmidl, Christian; Suzuki, Takahiro; Ntini, Evgenia; Arner, Erik; Valen, Eivind; Li, Kang; Schwarzfischer, Lucia; Glatz, Dagmar; Raithel, Johanna; Lilje, Berit; Rapin, Nicolas; Bagger, Frederik Otzen; Jørgensen, Mette; Andersen, Peter Refsing; Bertin, Nicolas; Rackham, Owen; Burroughs, A. Maxwell; Baillie, J. Kenneth; Ishizu, Yuri; Shimizu, Yuri; Furuhata, Erina; Maeda, Shiori; Negishi, Yutaka; Mungall, Christopher J.; Meehan, Terrence F.; Lassmann, Timo; Itoh, Masayoshi; Kawaji, Hideya; Kondo, Naoto; Kawai, Jun; Lennartsson, Andreas; Daub, Carsten O.; Heutink, Peter; Hume, David A.; Jensen, Torben Heick; Suzuki, Harukazu; Hayashizaki, Yoshihide; Müller, Ferenc; Consortium, The Fantom; Forrest, Alistair R. R.; Carninci, Piero; Rehli, Michael; Sandelin, Albin

2014-03-01

Enhancers control the correct temporal and cell-type-specific activation of gene expression in multicellular eukaryotes. Knowing their properties, regulatory activity and targets is crucial to understand the regulation of differentiation and homeostasis. Here we use the FANTOM5 panel of samples, covering the majority of human tissues and cell types, to produce an atlas of active, in vivo-transcribed enhancers. We show that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity. The atlas is used to compare regulatory programs between different cells at unprecedented depth, to identify disease-associated regulatory single nucleotide polymorphisms, and to classify cell-type-specific and ubiquitous enhancers. We further explore the utility of enhancer redundancy, which explains gene expression strength rather than expression patterns. The online FANTOM5 enhancer atlas represents a unique resource for studies on cell-type-specific enhancers and gene regulation.

Selective enhancement of carbohydrate ion abundances by diamond nanoparticles for mass spectrometric analysis.

PubMed

Wu, Chieh-Lin; Wang, Chia-Chen; Lai, Yin-Hung; Lee, Hsun; Lin, Jia-Der; Lee, Yuan Tseh; Wang, Yi-Sheng

2013-04-16

Diamond nanoparticles (DNPs) were incorporated into matrix-assisted laser desorption/ionization (MALDI) samples to enhance the sensitivity of the mass spectrometer to carbohydrates. The DNPs optimize the MALDI sample morphology and thermalize the samples for thermally labile compounds because they have a high thermal conductivity, a low extinction coefficient in UV-vis spectral range, and stable chemical properties. The best enhancement effect was achieved when matrix, DNP, and carbohydrate solutions were deposited and vacuum-dried consecutively to form a trilayer sample morphology. It allows the direct identification of underivatized carbohydrates mixed with equal amount of proteins because no increase in the ion abundance of proteins was achieved. For dextran with an average molecular weight of 1500, the trilayer method typically improves the sensitivity by 79- and 7-fold in comparison to the conventional dried-droplet and thin-layer methods, respectively.

Sol-gel chemical sensors for surface-enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Vincent Y.; Farquharson, Stuart; Kwon, Hueong-Chan; Shahriari, Mahmoud R.; Rainey, Petrie M.

1999-02-01

Surface-enhanced Raman spectroscopy (SERS) promises to be one of the most sensitive methods for chemical detection. Unfortunately, the inability of SERS to perform quantitative chemical analysis has slowed its general use in laboratories. This is largely due to the difficulty of manufacturing either active surfaces that yield reproducible enhancements, or surfaces that are capable of reversible chemical adsorption, or both. In an effort to meet this need, we have developed metal-doped sol-gels that provide surface-enhancement of Raman scattering. The porous silica network offers a unique environment for stabilizing SER active metal particles and the high surface area increases the interaction between the analyte and metal particles. This eliminates the need to concentrate the analyte on the surface by evaporating the solvent. The sol-gel is easily coated on a variety of surfaces, such as fiber optics, glass slides, or glass tubing, and can be designed into sample flow systems. Here we present the development of both gold- and silver-doped sol-gels, which have been used to coat the inside walls of glass sample vials for SERS applications. The performance of the metal-doped sol-gels was evaluated using p-aminobenzoic acid, to establish enhancement factors, detection limits, dynamic response range, reversibility, reproducibility, and suitability to commercial spectrometers. Measurements of trace chemicals, such as adenine and cocaine, are also presented.

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

"One-Stop Shop": Free-Breathing Dynamic Contrast-Enhanced Magnetic Resonance Imaging of the Kidney Using Iterative Reconstruction and Continuous Golden-Angle Radial Sampling.

PubMed

Riffel, Philipp; Zoellner, Frank G; Budjan, Johannes; Grimm, Robert; Block, Tobias K; Schoenberg, Stefan O; Hausmann, Daniel

2016-11-01

The purpose of the present study was to evaluate a recently introduced technique for free-breathing dynamic contrast-enhanced renal magnetic resonance imaging (MRI) applying a combination of radial k-space sampling, parallel imaging, and compressed sensing. The technique allows retrospective reconstruction of 2 motion-suppressed sets of images from the same acquisition: one with lower temporal resolution but improved image quality for subjective image analysis, and one with high temporal resolution for quantitative perfusion analysis. In this study, 25 patients underwent a kidney examination, including a prototypical fat-suppressed, golden-angle radial stack-of-stars T1-weighted 3-dimensional spoiled gradient-echo examination (GRASP) performed after contrast agent administration during free breathing. Images were reconstructed at temporal resolutions of 55 spokes per frame (6.2 seconds) and 13 spokes per frame (1.5 seconds). The GRASP images were evaluated by 2 blinded radiologists. First, the reconstructions with low temporal resolution underwent subjective image analysis: the radiologists assessed the best arterial phase and the best renal phase and rated image quality score for each patient on a 5-point Likert-type scale.In addition, the diagnostic confidence was rated according to a 3-point Likert-type scale. Similarly, respiratory motion artifacts and streak artifacts were rated according to a 3-point Likert-type scale.Then, the reconstructions with high temporal resolution were analyzed with a voxel-by-voxel deconvolution approach to determine the renal plasma flow, and the results were compared with values reported in previous literature. Reader 1 and reader 2 rated the overall image quality score for the best arterial phase and the best renal phase with a median image quality score of 4 (good image quality) for both phases, respectively. A high diagnostic confidence (median score of 3) was observed. There were no respiratory motion artifacts in any of the

SURFACTANT ENHANCED AQUIFER REMEDIATION WITH SURFACTANT REGENERATION/REUSE

EPA Science Inventory

A demonstration of surfactant-enhanced aquifer remediation was conducted during the spring of 1999 at Marine Corps Base, Camp LeJeune, NC. A PCE-DNAPL zone was identified and delineated by extensive soil sampling in 1997, and was further characteized by a partitioning interwell t...

Accuracy Enhancement of Raman Spectroscopy Using Complementary Laser-Induced Breakdown Spectroscopy (LIBS) with Geologically Mixed Samples.

PubMed

Choi, Soojin; Kim, Dongyoung; Yang, Junho; Yoh, Jack J

2017-04-01

Quantitative Raman analysis was carried out with geologically mixed samples that have various matrices. In order to compensate the matrix effect in Raman shift, laser-induced breakdown spectroscopy (LIBS) analysis was performed. Raman spectroscopy revealed the geological materials contained in the mixed samples. However, the analysis of a mixture containing different matrices was inaccurate due to the weak signal of the Raman shift, interference, and the strong matrix effect. On the other hand, the LIBS quantitative analysis of atomic carbon and calcium in mixed samples showed high accuracy. In the case of the calcite and gypsum mixture, the coefficient of determination of atomic carbon using LIBS was 0.99, while the signal using Raman was less than 0.9. Therefore, the geological composition of the mixed samples is first obtained using Raman and the LIBS-based quantitative analysis is then applied to the Raman outcome in order to construct highly accurate univariate calibration curves. The study also focuses on a method to overcome matrix effects through the two complementary spectroscopic techniques of Raman spectroscopy and LIBS.

Greater self-enhancement in Western than Eastern Ukraine, but failure to replicate the Muhammad Ali effect.

PubMed

Kemmelmeier, Markus; Malanchuk, Oksana

2016-02-01

Based on the cross-cultural research linking individualism-collectivism and self-enhancement, this research examines regional pattern of self-enhancement in Ukraine. Broadly speaking, the western part of Ukraine is mainly Ukrainian speaking and historically oriented towards Europe, whereas Eastern Ukraine is mainly Russian speaking and historically oriented towards the Russian cultural sphere. We found self-enhancement on a "better than average" task to be higher in a Western Ukrainian sample compared to an Eastern Ukrainian sample, with differences in independent self-construals supporting assumed regional variation in individualism. However, the Muhammad Ali effect, the finding that self-enhancement is greater in the domain of morality than intelligence, was not replicated. The discussion focuses on the specific sources of this regional difference in self-enhancement, and reasons for why the Muhammad Ali effect was not found. © 2015 International Union of Psychological Science.

A new sampling scheme for developing metamodels with the zeros of Chebyshev polynomials

NASA Astrophysics Data System (ADS)

Wu, Jinglai; Luo, Zhen; Zhang, Nong; Zhang, Yunqing

2015-09-01

The accuracy of metamodelling is determined by both the sampling and approximation. This article proposes a new sampling method based on the zeros of Chebyshev polynomials to capture the sampling information effectively. First, the zeros of one-dimensional Chebyshev polynomials are applied to construct Chebyshev tensor product (CTP) sampling, and the CTP is then used to construct high-order multi-dimensional metamodels using the 'hypercube' polynomials. Secondly, the CTP sampling is further enhanced to develop Chebyshev collocation method (CCM) sampling, to construct the 'simplex' polynomials. The samples of CCM are randomly and directly chosen from the CTP samples. Two widely studied sampling methods, namely the Smolyak sparse grid and Hammersley, are used to demonstrate the effectiveness of the proposed sampling method. Several numerical examples are utilized to validate the approximation accuracy of the proposed metamodel under different dimensions.

High-Field Liquid-State Dynamic Nuclear Polarization in Microliter Samples.

PubMed

Yoon, Dongyoung; Dimitriadis, Alexandros I; Soundararajan, Murari; Caspers, Christian; Genoud, Jeremy; Alberti, Stefano; de Rijk, Emile; Ansermet, Jean-Philippe

2018-05-01

Nuclear hyperpolarization in the liquid state by dynamic nuclear polarization (DNP) has been of great interest because of its potential use in NMR spectroscopy of small samples of biological and chemical compounds in aqueous media. Liquid state DNP generally requires microwave resonators in order to generate an alternating magnetic field strong enough to saturate electron spins in the solution. As a consequence, the sample size is limited to dimensions of the order of the wavelength, and this restricts the sample volume to less than 100 nL for DNP at 9 T (∼260 GHz). We show here a new approach that overcomes this sample size limitation. Large saturation of electron spins was obtained with a high-power (∼150 W) gyrotron without microwave resonators. Since high power microwaves can cause serious dielectric heating in polar solutions, we designed a planar probe which effectively alleviates dielectric heating. A thin liquid sample of 100 μm of thickness is placed on a block of high thermal conductivity aluminum nitride, with a gold coating that serves both as a ground plane and as a heat sink. A meander or a coil were used for NMR. We performed 1 H DNP at 9.2 T (∼260 GHz) and at room temperature with 10 μL of water, a volume that is more than 100× larger than reported so far. The 1 H NMR signal is enhanced by a factor of about -10 with 70 W of microwave power. We also demonstrated the liquid state of 31 P DNP in fluorobenzene containing triphenylphosphine and obtained an enhancement of ∼200.

Direct measurements of sample heating by a laser-induced air plasma in pre-ablation spark dual-pulse laser-induced breakdown spectroscopy (LIBS).

PubMed

Register, Janna; Scaffidi, Jonathan; Angel, S Michael

2012-08-01

Direct measurements of temperature changes were made using small thermocouples (TC), placed near a laser-induced air plasma. Temperature changes up to ~500 °C were observed. From the measured temperature changes, estimates were made of the amount of heat absorbed per unit area. This allowed calculations to be made of the surface temperature, as a function of time, of a sample heated by the air plasma that is generated during orthogonal pre-ablation spark dual-pulse (DP) LIBS measurements. In separate experiments, single-pulse (SP) LIBS emission and sample ablation rate measurements were performed on nickel at sample temperatures ranging from room temperature to the maximum surface temperature that was calculated using the TC measurement results (500 °C). A small, but real sample temperature-dependent increase in both SP LIBS emission and the rate of sample ablation was found for nickel samples heated up to 500 °C. Comparison of DP LIBS emission enhancement values for bulk nickel samples at room temperature versus the enhanced SP LIBS emission and sample ablation rates observed as a function of increasing sample temperature suggests that sample heating by the laser-induced air plasma plays only a minor role in DP LIBS emission enhancement.

Final LDRD report : development of sample preparation methods for ChIPMA-based imaging mass spectrometry of tissue samples.

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

Maharrey, Sean P.; Highley, Aaron M.; Behrens, Richard, Jr.

2007-12-01

The objective of this short-term LDRD project was to acquire the tools needed to use our chemical imaging precision mass analyzer (ChIPMA) instrument to analyze tissue samples. This effort was an outgrowth of discussions with oncologists on the need to find the cellular origin of signals in mass spectra of serum samples, which provide biomarkers for ovarian cancer. The ultimate goal would be to collect chemical images of biopsy samples allowing the chemical images of diseased and nondiseased sections of a sample to be compared. The equipment needed to prepare tissue samples have been acquired and built. This equipment includesmore » an cyro-ultramicrotome for preparing thin sections of samples and a coating unit. The coating unit uses an electrospray system to deposit small droplets of a UV-photo absorbing compound on the surface of the tissue samples. Both units are operational. The tissue sample must be coated with the organic compound to enable matrix assisted laser desorption/ionization (MALDI) and matrix enhanced secondary ion mass spectrometry (ME-SIMS) measurements with the ChIPMA instrument Initial plans to test the sample preparation using human tissue samples required development of administrative procedures beyond the scope of this LDRD. Hence, it was decided to make two types of measurements: (1) Testing the spatial resolution of ME-SIMS by preparing a substrate coated with a mixture of an organic matrix and a bio standard and etching a defined pattern in the coating using a liquid metal ion beam, and (2) preparing and imaging C. elegans worms. Difficulties arose in sectioning the C. elegans for analysis and funds and time to overcome these difficulties were not available in this project. The facilities are now available for preparing biological samples for analysis with the ChIPMA instrument. Some further investment of time and resources in sample preparation should make this a useful tool for chemical imaging applications.« less

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

Russel Howe of team Survey speaks with Sample Return Robot Challenge staff members after the team's robot failed to leave the starting platform during it's attempt at the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

Kenneth Stafford, Assistant Director of Robotics Engineering and Director of the Robotics Resource Center at the Worcester Polytechnic Institute (WPI), verifies the location of the target sample during the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

Members of the Mountaineers team from West Virginia University celebrate after their robot returned to the starting platform after picking up the sample during a rerun of the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

The effect of dose enhancement near metal interfaces on synthetic diamond based X-ray dosimeters

NASA Astrophysics Data System (ADS)

Alamoudi, D.; Lohstroh, A.; Albarakaty, H.

2017-11-01

This study investigates the effects of dose enhancement on the photocurrent performance at metallic interfaces in synthetic diamond detectors based X-ray dosimeters as a function of bias voltages. Monte Carlo (MC) simulations with the BEAMnrc code were carried out to simulate the dose enhancement factor (DEF) and compared against the equivalent photocurrent ratio from experimental investigations. The MC simulation results show that the sensitive region for the absorbed dose distribution covers a few micrometers distances from the interface. Experimentally, two single crystals (SC) and one polycrystalline (PC) synthetic diamond samples were fabricated into detectors with carbon based electrodes by boron and carbon ion implantation. Subsequently; the samples were each mounted inside a tissue equivalent encapsulation to minimize unintended fluence perturbation. Dose enhancement was generated by placing copper, lead or gold near the active volume of the detectors using 50 kVp and 100 kVp X-rays relevant for medical dosimetry. The results show enhancement in the detectors' photocurrent performance when different metals are butted up to the diamond bulk as expected. The variation in the photocurrent measurement depends on the type of diamond samples, their electrodes' fabrication and the applied bias voltages indicating that the dose enhancement near the detector may modify their electronic performance.

Enhanced NIF neutron activation diagnostics.

PubMed

Yeamans, C B; Bleuel, D L; Bernstein, L A

2012-10-01

The NIF neutron activation diagnostic suite relies on removable activation samples, leading to operational inefficiencies and a fundamental lower limit on the half-life of the activated product that can be observed. A neutron diagnostic system measuring activation of permanently installed samples could remove these limitations and significantly enhance overall neutron diagnostic capabilities. The physics and engineering aspects of two proposed systems are considered: one measuring the (89)Zr/(89 m)Zr isomer ratio in the existing Zr activation medium and the other using potassium zirconate as the activation medium. Both proposed systems could improve the signal-to-noise ratio of the current system by at least a factor of 5 and would allow independent measurement of fusion core velocity and fuel areal density.

STM-induced light emission enhanced by weakly coupled organic ad-layers

NASA Astrophysics Data System (ADS)

Cottin, M. C.; Ekici, E.; Bobisch, C. A.

2018-03-01

We analyze the light emission induced by the tunneling current flowing in a scanning tunneling microscopy experiment. In particular, we study the influence of organic ad-layers on the light emission on the initial monolayer of bismuth (Bi) on Cu(111) in comparison to the well-known case of organic ad-layers on Ag(111). On the Bi/Cu(111)-surface, we find that the scanning tunneling microscopy-induced light emission is considerably enhanced if an organic layer, e.g., the fullerene C60 or the perylene derivate perylene-tetracarboxylic-dianhydride, is introduced into the tip-sample junction. The enhancement can be correlated with a peculiarly weak interaction between the adsorbed molecules and the underlying Bi/Cu(111) substrate as compared to the Ag(111) substrate. This allows us to efficiently enhance and tune the coupling of the tunneling current to localized excitations of the tip-sample junction, which in turn couple to radiative decay channels.

Ab initio molecular dynamics with enhanced sampling for surface reaction kinetics at finite temperatures: CH2 ⇌ CH + H on Ni(111) as a case study

NASA Astrophysics Data System (ADS)

Sun, Geng; Jiang, Hong

2015-12-01

A comprehensive understanding of surface thermodynamics and kinetics based on first-principles approaches is crucial for rational design of novel heterogeneous catalysts, and requires combining accurate electronic structure theory and statistical mechanics modeling. In this work, ab initio molecular dynamics (AIMD) combined with the integrated tempering sampling (ITS) method has been explored to study thermodynamic and kinetic properties of elementary processes on surfaces, using a simple reaction CH 2 ⇌ CH + H on the Ni(111) surface as an example. By a careful comparison between the results from ITS-AIMD simulation and those evaluated in terms of the harmonic oscillator (HO) approximation, it is found that the reaction free energy and entropy from the HO approximation are qualitatively consistent with the results from ITS-AIMD simulation, but there are also quantitatively significant discrepancies. In particular, the HO model misses the entropy effects related to the existence of multiple adsorption configurations arising from the frustrated translation and rotation motion of adsorbed species, which are different in the reactant and product states. The rate constants are evaluated from two ITS-enhanced approaches, one using the transition state theory (TST) formulated in terms of the potential of mean force (PMF) and the other one combining ITS with the transition path sampling (TPS) technique, and are further compared to those based on harmonic TST. It is found that the rate constants from the PMF-based TST are significantly smaller than those from the harmonic TST, and that the results from PMF-TST and ITS-TPS are in a surprisingly good agreement. These findings indicate that the basic assumptions of transition state theory are valid in such elementary surface reactions, but the consideration of statistical averaging of all important adsorption configurations and reaction pathways, which are missing in the harmonic TST, are critical for

Technology-Enhanced Consultation in Counselling: A Comparative Study

ERIC Educational Resources Information Center

Astramovich, Randall L.; Jones, W. Paul; Coker, J. Kelly

2004-01-01

Two quasi-experimental studies comparing technology-enhanced counselling consultation were conducted with a sample of 147 students enrolled in an undergraduate counselling and consultation course for elementary and secondary teachers. Study 1 (N = 76) compared the effectiveness of counselling consultation using telephone, text chat, or text chat…

Enhanced optical coupling and Raman scattering via microscopic interface engineering

NASA Astrophysics Data System (ADS)

Thompson, Jonathan V.; Hokr, Brett H.; Kim, Wihan; Ballmann, Charles W.; Applegate, Brian E.; Jo, Javier A.; Yamilov, Alexey; Cao, Hui; Scully, Marlan O.; Yakovlev, Vladislav V.

2017-11-01

Spontaneous Raman scattering is an extremely powerful tool for the remote detection and identification of various chemical materials. However, when those materials are contained within strongly scattering or turbid media, as is the case in many biological and security related systems, the sensitivity and range of Raman signal generation and detection is severely limited. Here, we demonstrate that through microscopic engineering of the optical interface, the optical coupling of light into a turbid material can be substantially enhanced. This improved coupling facilitates the enhancement of the Raman scattering signal generated by molecules within the medium. In particular, we detect at least two-orders of magnitude more spontaneous Raman scattering from a sample when the pump laser light is focused into a microscopic hole in the surface of the sample. Because this approach enhances both the interaction time and interaction region of the laser light within the material, its use will greatly improve the range and sensitivity of many spectroscopic techniques, including Raman scattering and fluorescence emission detection, inside highly scattering environments.

Enhancement of Permeation in Transdermal Drug Delivery System by 6μm Wavelength Area Using an MIR-FEL

NASA Astrophysics Data System (ADS)

Uchizono, T.; Ishii, K.; Iwao, Y.; Itou, Y.; Maruo, H.; Hori, M.; Awazu, K.

2005-03-01

Ablation of the stratum corneum (SC) by pulsed-laser irradiation is one method of enhancing transdermal drug delivery (TD). For non-invasive laser TD treatment, we have tried to enhance TD without ablation of the SC using an MIR-FEL (6-μm wavelength) (FEL : free electron laser). Lidocaine was used as the drug in this study. The enhancement of TD was measured by HPLC. It was found that the lidocaine TD of the sample irradiated by MIR-FEL was enhanced 10 fold faster than the non-irradiated sample with a flux at 0.5 μg/cm2/h, measured by HPLC. We have demonstrated the effectiveness of TD enhancement by an MIR-FEL (6-μm wavelength) irradiation.

Improvements to Nuclear Data and Its Uncertainties by Theoretical Modeling

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

Danon, Yaron; Nazarewicz, Witold; Talou, Patrick

2013-02-18

This project addresses three important gaps in existing evaluated nuclear data libraries that represent a significant hindrance against highly advanced modeling and simulation capabilities for the Advanced Fuel Cycle Initiative (AFCI). This project will: Develop advanced theoretical tools to compute prompt fission neutrons and gamma-ray characteristics well beyond average spectra and multiplicity, and produce new evaluated files of U and Pu isotopes, along with some minor actinides; Perform state-of-the-art fission cross-section modeling and calculations using global and microscopic model input parameters, leading to truly predictive fission cross-sections capabilities. Consistent calculations for a suite of Pu isotopes will be performed; Implementmore » innovative data assimilation tools, which will reflect the nuclear data evaluation process much more accurately, and lead to a new generation of uncertainty quantification files. New covariance matrices will be obtained for Pu isotopes and compared to existing ones. The deployment of a fleet of safe and efficient advanced reactors that minimize radiotoxic waste and are proliferation-resistant is a clear and ambitious goal of AFCI. While in the past the design, construction and operation of a reactor were supported through empirical trials, this new phase in nuclear energy production is expected to rely heavily on advanced modeling and simulation capabilities. To be truly successful, a program for advanced simulations of innovative reactors will have to develop advanced multi-physics capabilities, to be run on massively parallel super- computers, and to incorporate adequate and precise underlying physics. And all these areas have to be developed simultaneously to achieve those ambitious goals. Of particular interest are reliable fission cross-section uncertainty estimates (including important correlations) and evaluations of prompt fission neutrons and gamma-ray spectra and uncertainties.« less

Improvements to sample processing and measurement to enable more widespread environmental application of tritium

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

Moran, James; Alexander, Thomas; Aalseth, Craig

2017-08-01

Previous measurements have demonstrated the wealth of information that tritium (T) can provide on environmentally relevant processes. We present modifications to sample preparation approaches that enable T measurement by proportional counting on small sample sizes equivalent to 120 mg of water and demonstrate the accuracy of these methods on a suite of standardized water samples. This enhanced method should provide the analytical flexibility needed to address persistent knowledge gaps in our understanding of T behavior in the environment.

Integration of stable isotope and trace contaminant concentration for enhanced forensic acetone discrimination.

PubMed

Moran, James J; Ehrhardt, Christopher J; Wahl, Jon H; Kreuzer, Helen W; Wahl, Karen L

2013-11-15

We analyzed 21 neat acetone samples from 15 different suppliers to demonstrate the utility of a coupled stable isotope and trace contaminant strategy for distinguishing forensically-relevant samples. By combining these two pieces of orthogonal data we could discriminate all of the acetones that were produced by the 15 different suppliers. Using stable isotope ratios alone, we were able to distinguish 8 acetone samples, while the remaining 13 fell into four clusters with highly similar signatures. Adding trace chemical contaminant information enhanced discrimination to 13 individual acetones with three residual clusters. The acetones within each cluster shared a common manufacturer and might, therefore, not be expected to be resolved. The data presented here demonstrates the power of combining orthogonal data sets to enhance sample fingerprinting and highlights the role disparate data could play in future forensic investigations. © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

An investigation of potential applications of OP-SAPS: Operational Sampled Analog Processors

NASA Technical Reports Server (NTRS)

Parrish, E. A.; Mcvey, E. S.

1977-01-01

The application of OP-SAP's (operational sampled analog processors) in pattern recognition system is summarized. Areas investigated include: (1) human face recognition; (2) a high-speed programmable transversal filter system; (3) discrete word (speech) recognition; and (4) a resolution enhancement system.

GUIDELINES FOR INSTALLATION AND SAMPLING OF SUB-SLAB VAPOR PROBES TO SUPPORT ASSESSMENT OF VAPOR INTRUSION

EPA Science Inventory

The purpose of this paper is to provide guidelines for sub-slab sampling using dedicated vapor probes. Use of dedicated vapor probes allows for multiple sample events before and after corrective action and for vacuum testing to enhance the design and monitoring of a corrective m...

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

Team KuuKulgur watches as their robots attempt the level one competition during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

Sam Ortega, NASA program manager for Centennial Challenges, is seen during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

The Retrievers team robot is seen as it attempts the level one challenge the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

Raman signal enhancement by multiple beam excitation and its application for the detection of chemicals

NASA Astrophysics Data System (ADS)

Gupta, Sakshi; Ahmad, Azeem; Gambhir, Vijayeta; Reddy, Martha N.; Mehta, Dalip S.

2015-08-01

In a typical Raman based sensor, a single laser beam is used for exciting the sample and the backscattered or forward scattered light is collected using collection optics and is analyzed by a spectrometer. We have investigated that by means of exciting the sample with multiple beams, i.e., by dividing the same input power of the single beam into two or three or more beams and exciting the sample from different angles, the Raman signal enhances significantly. Due to the presence of multiple beams passing through the same volume of the sample, an interference pattern is formed and the volume of interaction of excitation beams with the sample increases. By means of this geometry, the enhancement in the Raman signal is observed and it was found that the signal strength increases linearly with the increase in number of excitation beams. Experimental results of this scheme for excitation of the samples are reported for explosive detection at a standoff distance.

STP K Basin Sludge Sample Archive at the Pacific Northwest National Laboratory FY2014

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

Fiskum, Sandra K.; Smoot, Margaret R.; Schmidt, Andrew J.

2014-06-01

The Pacific Northwest National Laboratory (PNNL) currently houses 88 samples (~10.5 kg) of K Basin sludge (81 wet and seven dry samples) on behalf of the Sludge Treatment Project (STP), which is managed for the U.S. Department of Energy (DOE) by the CH2M Hill Plateau Remediation Company (CHPRC). Selected samples are intended to serve, in part, as sentinels to enhance understanding of sludge properties after long-term storage, and thus enhance understanding of sludge behavior following transfer to sludge transfer and storage containers (STSCs) and storage at the Hanford 200 Area central plateau. In addition, remaining samples serve in contingency formore » future testing requirements. At PNNL, the samples are tracked and maintained under a prescriptive and disciplined monthly sample-monitoring program implemented by PNNL staff. This report updates the status of the K Basin archive sludge sample inventory to April 2014. The previous inventory status report, PNNL 22245 (Fiskum et al. 2013, limited distribution report), was issued in February of 2013. This update incorporates changes in the inventory related to repackaging of 17 samples under test instructions 52578 TI052, K Basin Sludge Sample Repackaging for Continued Long Term Storage, and 52578 TI053, K Basin Sludge Sample Repackaging Post-2014 Shear Strength Measurements. Note that shear strength measurement results acquired in 2014 are provided separately. Specifically, this report provides the following: • a description of the K Basin sludge sample archive program and the sample inventory • a summary and images of the samples that were repackaged in April 2014 • up-to-date images and plots of the settled density and water loss from all applicable samples in the inventory • updated sample pedigree charts, which provide a roadmap of the genesis and processing history of each sample in the inventory • occurrence and deficiency reports associated with sample storage and repackaging« less

Rapid Sampling of Molecules via Skin for Diagnostic and Forensic Applications

PubMed Central

Paliwal, Sumit; Ogura, Makoto

2010-01-01

ABSTRACT Purpose Skin provides an excellent portal for diagnostic monitoring of a variety of entities; however, there is a dearth of reliable methods for patient-friendly sampling of skin constituents. This study describes the use of low-frequency ultrasound as a one-step methodology for rapid sampling of molecules from the skin. Methods Sampling was performed using a brief exposure of 20 kHz ultrasound to skin in the presence of a sampling fluid. In vitro sampling from porcine skin was performed to assess the effectiveness of the method and its ability to sample drugs and endogenous epidermal biomolecules from the skin. Dermal presence of an antifungal drug—fluconazole and an abused substance, cocaine—was assessed in rats. Results Ultrasonic sampling captured the native profile of various naturally occurring moisturizing factors in skin. A high sampling efficiency (79 ± 13%) of topically delivered drug was achieved. Ultrasound consistently sampled greater amounts of drug from the skin compared to tape stripping. Ultrasonic sampling also detected sustained presence of cocaine in rat skin for up to 7 days as compared to its rapid disappearance from the urine. Conclusions Ultrasonic sampling provides significant advantages including enhanced sampling from deeper layers of skin and high temporal sampling sensitivity. PMID:20238151

Advantages of Unfair Quantum Ground-State Sampling.

PubMed

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

2017-04-21

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

Method for Operating a Sensor to Differentiate Between Analytes in a Sample

DOEpatents

Kunt, Tekin; Cavicchi, Richard E; Semancik, Stephen; McAvoy, Thomas J

1998-07-28

Disclosed is a method for operating a sensor to differentiate between first and second analytes in a sample. The method comprises the steps of determining a input profile for the sensor which will enhance the difference in the output profiles of the sensor as between the first analyte and the second analyte; determining a first analyte output profile as observed when the input profile is applied to the sensor; determining a second analyte output profile as observed when the temperature profile is applied to the sensor; introducing the sensor to the sample while applying the temperature profile to the sensor, thereby obtaining a sample output profile; and evaluating the sample output profile as against the first and second analyte output profiles to thereby determine which of the analytes is present in the sample.

Interactions among resource partitioning, sampling effect, and facilitation on the biodiversity effect: a modeling approach.

PubMed

Flombaum, Pedro; Sala, Osvaldo E; Rastetter, Edward B

2014-02-01

Resource partitioning, facilitation, and sampling effect are the three mechanisms behind the biodiversity effect, which is depicted usually as the effect of plant-species richness on aboveground net primary production. These mechanisms operate simultaneously but their relative importance and interactions are difficult to unravel experimentally. Thus, niche differentiation and facilitation have been lumped together and separated from the sampling effect. Here, we propose three hypotheses about interactions among the three mechanisms and test them using a simulation model. The model simulated water movement through soil and vegetation, and net primary production mimicking the Patagonian steppe. Using the model, we created grass and shrub monocultures and mixtures, controlled root overlap and grass water-use efficiency (WUE) to simulate gradients of biodiversity, resource partitioning and facilitation. The presence of shrubs facilitated grass growth by increasing its WUE and in turn increased the sampling effect, whereas root overlap (resource partitioning) had, on average, no effect on sampling effect. Interestingly, resource partitioning and facilitation interacted so the effect of facilitation on sampling effect decreased as resource partitioning increased. Sampling effect was enhanced by the difference between the two functional groups in their efficiency in using resources. Morphological and physiological differences make one group outperform the other; once these differences were established further differences did not enhance the sampling effect. In addition, grass WUE and root overlap positively influence the biodiversity effect but showed no interactions.

Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment

NASA Astrophysics Data System (ADS)

Lv, Chao; Zheng, Lianqing; Yang, Wei

2012-01-01

Molecular dynamics sampling can be enhanced via the promoting of potential energy fluctuations, for instance, based on a Hamiltonian modified with the addition of a potential-energy-dependent biasing term. To overcome the diffusion sampling issue, which reveals the fact that enlargement of event-irrelevant energy fluctuations may abolish sampling efficiency, the essential energy space random walk (EESRW) approach was proposed earlier. To more effectively accelerate the sampling of solute conformations in aqueous environment, in the current work, we generalized the EESRW method to a two-dimension-EESRW (2D-EESRW) strategy. Specifically, the essential internal energy component of a focused region and the essential interaction energy component between the focused region and the environmental region are employed to define the two-dimensional essential energy space. This proposal is motivated by the general observation that in different conformational events, the two essential energy components have distinctive interplays. Model studies on the alanine dipeptide and the aspartate-arginine peptide demonstrate sampling improvement over the original one-dimension-EESRW strategy; with the same biasing level, the present generalization allows more effective acceleration of the sampling of conformational transitions in aqueous solution. The 2D-EESRW generalization is readily extended to higher dimension schemes and employed in more advanced enhanced-sampling schemes, such as the recent orthogonal space random walk method.

Multispectral and Panchromatic used Enhancement Resolution and Study Effective Enhancement on Supervised and Unsupervised Classification Land – Cover

NASA Astrophysics Data System (ADS)

Salman, S. S.; Abbas, W. A.

2018-05-01

The goal of the study is to support analysis Enhancement of Resolution and study effect on classification methods on bands spectral information of specific and quantitative approaches. In this study introduce a method to enhancement resolution Landsat 8 of combining the bands spectral of 30 meters resolution with panchromatic band 8 of 15 meters resolution, because of importance multispectral imagery to extracting land - cover. Classification methods used in this study to classify several lands -covers recorded from OLI- 8 imagery. Two methods of Data mining can be classified as either supervised or unsupervised. In supervised methods, there is a particular predefined target, that means the algorithm learn which values of the target are associated with which values of the predictor sample. K-nearest neighbors and maximum likelihood algorithms examine in this work as supervised methods. In other hand, no sample identified as target in unsupervised methods, the algorithm of data extraction searches for structure and patterns between all the variables, represented by Fuzzy C-mean clustering method as one of the unsupervised methods, NDVI vegetation index used to compare the results of classification method, the percent of dense vegetation in maximum likelihood method give a best results.

Enhanced bacterial affinity of PVDF membrane: its application as improved sea water sampling tool for environmental monitoring.

PubMed

Kumar, Sweta Binod; Sharnagat, Preeti; Manna, Paramita; Bhattacharya, Amit; Haldar, Soumya

2017-02-01

Isolation of diversified bacteria from seawater is a major challenge in the field of environmental microbiology. In the present study, an attempt has been made to select specific membrane with improved property of attaching diversified bacteria. Initially, different concentrations (15, 18, and 20% W/W) of polysulfone (PSF) were used to check their affinity for the attachment of selected gram-positive (Bacillus subtilis) and gram-negative (Escherichia coli) bacteria. Among these, 20% W/W PSF showed maximum attachment. Therefore, membrane prepared with other materials such as polyvinylidene fluoride (PVDF) and polyether sulfone (PES) were used with the same concentration (20% W/W) to check their improved bacterial attachment property. Comparative study of bacterial attachment on three different membranes revealed that PVDF possessed the highest affinity towards both the groups of bacteria. This property was confirmed by different analytical methods viz. contact angle, atomic force microscopy, zeta potential, and flux study and further validated with seawater samples collected from seven sites of western coast and Lakshadweep island of India, using Biolog EcoPlate™. All the samples showed that bacterial richness and diversity was high in PVDF membrane in comparison to surrounding seawater samples. Interestingly, affinity for more diversified bacteria was reported to be higher in water sample with less turbidity and low bacteria load. This finding can facilitate the development of PVDF (20% W/W) membrane as a simple, cheap, and less labor intensive environmental sampling tool for the isolation of diversified bacteria from seawater sample wih different physiochemical properties. Graphical abstract ᅟ.

Enhanced Photocatalytic Property of Cu Doped Sodium Niobate

DOE PAGES

Xu, Jianbin; Zhang, Feng; Sun, Bingyang; ...

2015-01-01

Here, we investigate the photocatalytic activity of Cu doped NaNbO 3 powder sample prepared by the modified polymer complex method. The photocatalytic activity of hydrogen evolution from methanol aqueous solution was improved by Cu 2.6 at% doping. The photocatalytic degradation of rhodamine B (RhB) under visible light irradiation was enhanced in comparison with pristine NaNbO 3. Cu introduction improved the adsorption property of NaNbO 3, judging from the Fourier transform infrared spectra. Moreover, the ultraviolet light excitation in Cu doped sample would accelerate the mineralized process.

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

PubMed

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-06-15

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

PubMed Central

Iida, Shinji; Nakamura, Haruki; Higo, Junichi

2016-01-01

We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein–protein or protein–ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. PMID:27288028

The NKI-Rockland Sample: A Model for Accelerating the Pace of Discovery Science in Psychiatry

PubMed Central

Nooner, Kate Brody; Colcombe, Stanley J.; Tobe, Russell H.; Mennes, Maarten; Benedict, Melissa M.; Moreno, Alexis L.; Panek, Laura J.; Brown, Shaquanna; Zavitz, Stephen T.; Li, Qingyang; Sikka, Sharad; Gutman, David; Bangaru, Saroja; Schlachter, Rochelle Tziona; Kamiel, Stephanie M.; Anwar, Ayesha R.; Hinz, Caitlin M.; Kaplan, Michelle S.; Rachlin, Anna B.; Adelsberg, Samantha; Cheung, Brian; Khanuja, Ranjit; Yan, Chaogan; Craddock, Cameron C.; Calhoun, Vincent; Courtney, William; King, Margaret; Wood, Dylan; Cox, Christine L.; Kelly, A. M. Clare; Di Martino, Adriana; Petkova, Eva; Reiss, Philip T.; Duan, Nancy; Thomsen, Dawn; Biswal, Bharat; Coffey, Barbara; Hoptman, Matthew J.; Javitt, Daniel C.; Pomara, Nunzio; Sidtis, John J.; Koplewicz, Harold S.; Castellanos, Francisco Xavier; Leventhal, Bennett L.; Milham, Michael P.

2012-01-01

The National Institute of Mental Health strategic plan for advancing psychiatric neuroscience calls for an acceleration of discovery and the delineation of developmental trajectories for risk and resilience across the lifespan. To attain these objectives, sufficiently powered datasets with broad and deep phenotypic characterization, state-of-the-art neuroimaging, and genetic samples must be generated and made openly available to the scientific community. The enhanced Nathan Kline Institute-Rockland Sample (NKI-RS) is a response to this need. NKI-RS is an ongoing, institutionally centered endeavor aimed at creating a large-scale (N > 1000), deeply phenotyped, community-ascertained, lifespan sample (ages 6–85 years old) with advanced neuroimaging and genetics. These data will be publically shared, openly, and prospectively (i.e., on a weekly basis). Herein, we describe the conceptual basis of the NKI-RS, including study design, sampling considerations, and steps to synchronize phenotypic and neuroimaging assessment. Additionally, we describe our process for sharing the data with the scientific community while protecting participant confidentiality, maintaining an adequate database, and certifying data integrity. The pilot phase of the NKI-RS, including challenges in recruiting, characterizing, imaging, and sharing data, is discussed while also explaining how this experience informed the final design of the enhanced NKI-RS. It is our hope that familiarity with the conceptual underpinnings of the enhanced NKI-RS will facilitate harmonization with future data collection efforts aimed at advancing psychiatric neuroscience and nosology. PMID:23087608

Digital staining for histopathology multispectral images by the combined application of spectral enhancement and spectral transformation.

PubMed

Bautista, Pinky A; Yagi, Yukako

2011-01-01

In this paper we introduced a digital staining method for histopathology images captured with an n-band multispectral camera. The method consisted of two major processes: enhancement of the original spectral transmittance and the transformation of the enhanced transmittance to its target spectral configuration. Enhancement is accomplished by shifting the original transmittance with the scaled difference between the original transmittance and the transmittance estimated with m dominant principal component (PC) vectors;the m-PC vectors were determined from the transmittance samples of the background image. Transformation of the enhanced transmittance to the target spectral configuration was done using an nxn transformation matrix, which was derived by applying a least square method to the enhanced and target spectral training data samples of the different tissue components. Experimental results on the digital conversion of a hematoxylin and eosin (H&E) stained multispectral image to its Masson's trichrome stained (MT) equivalent shows the viability of the method.

Feasibility Assessment of CO2 Sequestration and Enhanced Recovery in Gas Shale Reservoirs

NASA Astrophysics Data System (ADS)

Vermylen, J. P.; Hagin, P. N.; Zoback, M. D.

2008-12-01

CO2 sequestration and enhanced methane recovery may be feasible in unconventional, organic-rich, gas shale reservoirs in which the methane is stored as an adsorbed phase. Previous studies have shown that organic-rich, Appalachian Devonian shales adsorb approximately five times more carbon dioxide than methane at reservoir conditions. However, the enhanced recovery and sequestration concept has not yet been tested for gas shale reservoirs under realistic flow and production conditions. Using the lessons learned from previous studies on enhanced coalbed methane (ECBM) as a starting point, we are conducting laboratory experiments, reservoir modeling, and fluid flow simulations to test the feasibility of sequestration and enhanced recovery in gas shales. Our laboratory work investigates both adsorption and mechanical properties of shale samples to use as inputs for fluid flow simulation. Static and dynamic mechanical properties of shale samples are measured using a triaxial press under realistic reservoir conditions with varying gas saturations and compositions. Adsorption is simultaneously measured using standard, static, volumetric techniques. Permeability is measured using pulse decay methods calibrated to standard Darcy flow measurements. Fluid flow simulations are conducted using the reservoir simulator GEM that has successfully modeled enhanced recovery in coal. The results of the flow simulation are combined with the laboratory results to determine if enhanced recovery and CO2 sequestration is feasible in gas shale reservoirs.

Green design application on campus to enhance student’s quality of life

NASA Astrophysics Data System (ADS)

Tamiami, H.; Khaira, F.; Fachrudin, A.

2018-02-01

Green design becomes an important thing to applied in the building. Green building will provide comfortability and enhance Quality of Life (QoL) for the users. The purpose of this research is to analyze how green design application on campus to enhance student’s QoL. This research conducted in three campuses which located in North Sumatera Province, namely Universitas Sumatera Utara (USU), Universitas Negeri Medan (Unimed) and Universitas Medan Area (UMA) which have a lot of vegetation, open space, and multi-mass buildings. This research compared the green design application to QoL from three universities. Green design in this research that become independent variables focus on the energy efficiency and conservation (EEC), indoor health and comfort (IHC) and building environment management (BEM) with dependent variable is QoL. This research uses quantitative methods with questionnaire survey techniques. The population is students from the three universities with the sample of each University is 50 samples. The analysis uses multiple regression analysis. The results show that green design application may enhance QoL of students. The campus should have a good green design application to enhance QoL of students and give them comfortability.

An efficient implementation of Forward-Backward Least-Mean-Square Adaptive Line Enhancers

NASA Technical Reports Server (NTRS)

Yeh, H.-G.; Nguyen, T. M.

1995-01-01

An efficient implementation of the forward-backward least-mean-square (FBLMS) adaptive line enhancer is presented in this article. Without changing the characteristics of the FBLMS adaptive line enhancer, the proposed implementation technique reduces multiplications by 25% and additions by 12.5% in two successive time samples in comparison with those operations of direct implementation in both prediction and weight control. The proposed FBLMS architecture and algorithm can be applied to digital receivers for enhancing signal-to-noise ratio to allow fast carrier acquisition and tracking in both stationary and nonstationary environments.

Typing DNA profiles from previously enhanced fingerprints using direct PCR.

PubMed

Templeton, Jennifer E L; Taylor, Duncan; Handt, Oliva; Linacre, Adrian

2017-07-01

Fingermarks are a source of human identification both through the ridge patterns and DNA profiling. Typing nuclear STR DNA markers from previously enhanced fingermarks provides an alternative method of utilising the limited fingermark deposit that can be left behind during a criminal act. Dusting with fingerprint powders is a standard method used in classical fingermark enhancement and can affect DNA data. The ability to generate informative DNA profiles from powdered fingerprints using direct PCR swabs was investigated. Direct PCR was used as the opportunity to generate usable DNA profiles after performing any of the standard DNA extraction processes is minimal. Omitting the extraction step will, for many samples, be the key to success if there is limited sample DNA. DNA profiles were generated by direct PCR from 160 fingermarks after treatment with one of the following dactyloscopic fingerprint powders: white hadonite; silver aluminium; HiFi Volcano silk black; or black magnetic fingerprint powder. This was achieved by a combination of an optimised double-swabbing technique and swab media, omission of the extraction step to minimise loss of critical low-template DNA, and additional AmpliTaq Gold ® DNA polymerase to boost the PCR. Ninety eight out of 160 samples (61%) were considered 'up-loadable' to the Australian National Criminal Investigation DNA Database (NCIDD). The method described required a minimum of working steps, equipment and reagents, and was completed within 4h. Direct PCR allows the generation of DNA profiles from enhanced prints without the need to increase PCR cycle numbers beyond manufacturer's recommendations. Particular emphasis was placed on preventing contamination by applying strict protocols and avoiding the use of previously used fingerprint brushes. Based on this extensive survey, the data provided indicate minimal effects of any of these four powders on the chance of obtaining DNA profiles from enhanced fingermarks. Copyright © 2017

Enhanced coagulation for turbidity and Total Organic Carbon (TOC) removal from river Kansawati water.

PubMed

Narayan, Sumit; Goel, Sudha

2011-01-01

The objective of this study was to determine optimum coagulant doses for turbidity and Total Organic Carbon (TOC) removal and evaluate the extent to which TOC can be removed by enhanced coagulation. Jar tests were conducted in the laboratory to determine optimum doses of alum for the removal of turbidity and Natural Organic Matter (NOM) from river water. Various other water quality parameters were measured before and after thejar tests and included: UV Absorbance (UVA) at 254 nm, microbial concentrations, TDS, conductivity, hardness, alkalinity, and pH. The optimum alum dose for removal of turbidity and TOC was 20 mg/L for the sample collected in November 2009 and 100 mg/L for the sample collected in March 2010. In both cases, the dose for enhanced coagulation was significantly higher than that for conventional coagulation. The gain in TOC removal was insignificant compared to the increase in coagulant dose required. This is usual for low TOC (< 2 mg/L)--high alkalinity water. Other water samples with higher TOC need to be tested to demonstrate the effectiveness of enhanced coagulation.

Enhancement of the Probabilistic CEramic Matrix Composite ANalyzer (PCEMCAN) Computer Code

NASA Technical Reports Server (NTRS)

Shah, Ashwin

2000-01-01

This report represents a final technical report for Order No. C-78019-J entitled "Enhancement of the Probabilistic Ceramic Matrix Composite Analyzer (PCEMCAN) Computer Code." The scope of the enhancement relates to including the probabilistic evaluation of the D-Matrix terms in MAT2 and MAT9 material properties card (available in CEMCAN code) for the MSC/NASTRAN. Technical activities performed during the time period of June 1, 1999 through September 3, 1999 have been summarized, and the final version of the enhanced PCEMCAN code and revisions to the User's Manual is delivered along with. Discussions related to the performed activities were made to the NASA Project Manager during the performance period. The enhanced capabilities have been demonstrated using sample problems.

Enhancement of indirect sulphation of limestone by steam addition.

PubMed

Stewart, Michael C; Manovic, Vasilije; Anthony, Edward J; Macchi, Arturo

2010-11-15

The effect of water (H₂O(g)) on in situ SO₂ capture using limestone injection under (FBC) conditions was studied using a thermobalance and tube furnace. The indirect sulphation reaction was found to be greatly enhanced in the presence of H₂O(g). Stoichiometric conversion of samples occurred when sulphated with a synthetic flue gas containing 15% H₂O(g) in under 10 h, which is equivalent to a 45% increase in conversion as compared to sulphation without H₂O(g). Using gas pycnometry and nitrogen adsorption methods, it was shown that limestone samples sulphated in the presence of H₂O(g) undergo increased particle densification without any significant changes to pore area or volume. The microstructural changes and observed increase in conversion were attributed to enhanced solid-state diffusion in CaO/CaSO₄ in the presence of H₂O(g). Given steam has been shown to have such a strong influence on sulphation, whereas it had been previously regarded as inert, may prompt a revisiting of the classically accepted sulphation models and phenomena. These findings also suggest that steam injection may be used to enhance sulfur capture performance in fluidized beds firing low-moisture fuels such as petroleum coke.

Integration of Apollo Lunar Sample Data into Google Moon

NASA Technical Reports Server (NTRS)

Dawson, Melissa D.; Todd, Nancy S.; Lofgren, Gary

2010-01-01

The Google Moon Apollo Lunar Sample Data Integration project is a continuation of the Apollo 15 Google Moon Add-On project, which provides a scientific and educational tool for the study of the Moon and its geologic features. The main goal of this project is to provide a user-friendly interface for an interactive and educational outreach and learning tool for the Apollo missions. Specifically, this project?s focus is the dissemination of information about the lunar samples collected during the Apollo missions by providing any additional information needed to enhance the Apollo mission data on Google Moon. Apollo missions 15 and 16 were chosen to be completed first due to the availability of digitized lunar sample photographs and the amount of media associated with these missions. The user will be able to learn about the lunar samples collected in these Apollo missions, as well as see videos, pictures, and 360 degree panoramas of the lunar surface depicting the lunar samples in their natural state, following collection and during processing at NASA. Once completed, these interactive data layers will be submitted for inclusion into the Apollo 15 and 16 missions on Google Moon.

Self-enhancement among Westerners and Easterners: a cultural neuroscience approach

PubMed Central

Cai, Huajian; Shi, Yuanyuan; Gu, Ruolei; Sedikides, Constantine

2016-01-01

We adopted a cultural neuroscience approach to the investigation of self-enhancement. Western and Eastern participants made self-referent judgments on positive and negative traits while we recorded their electroencephalography signals. At the judgmental level, we assessed trait endorsement (judgments of traits self-descriptiveness) and reaction times (speed of such judgments). Participants endorsed more positive traits as self-descriptive and more negative traits as non-self-descriptive, although the magnitude of this effect (level of self-positivity) was higher in the Western than Eastern sample. Moreover, all participants responded faster to positive self-descriptive traits and to negative non-self-descriptive traits, indicating that the self-enhancement motive is equally potent across cultures. At the neurophysiological level, we assessed N170 and LPP. Negative traits elicited larger N170 among Easterners, indicating initial allocation of attentional resources to the processing of negative information. However, negative compared to positive self-descriptive traits elicited a larger LPP, whereas negative and positive non-self-descriptive traits did not differ in the LPP they elicited. This pattern generalized across samples, pointing to a pancultural physiological correlate of the self-enhancement motive. PMID:27217110

Applications of reversible covalent chemistry in analytical sample preparation.

PubMed

Siegel, David

2012-12-07

Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-10

A team KuuKulgur Robot from Estonia is seen on the practice field during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Tuesday, June 10, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Team KuuKulgur is one of eighteen teams competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

Sam Ortega, NASA program manager of Centennial Challenges, watches as robots attempt the rerun of the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

The University of California Santa Cruz Rover Team prepares their rover for the rerun of the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

Worcester Polytechnic Institute (WPI) President Laurie Leshin, speaks at a breakfast opening the TouchTomorrow Festival, held in conjunction with the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

The team AERO robot drives off the starting platform during the level one competition at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

Team Cephal's robot is seen on the starting platform during a rerun of the level one challenge at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

David Miller, NASA Chief Technologist, speaks at a breakfast opening the TouchTomorrow Festival, held in conjunction with the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

The Oregon State University Mars Rover Team's robot is seen during level one competition at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-10

Jerry Waechter of team Middleman from Dunedin, Florida, works on their robot named Ro-Bear during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Tuesday, June 10, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Team Middleman is one of eighteen teams competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

A robot from the Intrepid Systems team is seen during the rerun of the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

A team KuuKulgur robot is seen as it begins the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

The team Mountaineers robot is seen as it attempts the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

Members of the Oregon State University Mars Rover Team prepare their robot to attempt the level one competition at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

The Stellar Automation Systems team poses for a picture with their robot after attempting the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

The team Survey robot is seen as it conducts a demonstration of the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

All four of team KuuKulgur's robots are seen as they attempt the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

Spectators watch as the team Survey robot conducts a demonstration of the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

Team Middleman's robot, Ro-Bear, is seen as it starts the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

Two of team KuuKulgur's robots are seen as they attempt a rerun of the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

A robot from the University of Waterloo Robotics Team is seen during the rerun of the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

Members of team Survey follow their robot as it conducts a demonstration of the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

The entrance to Institute Park is seen during the level one challenge as during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

Sam Ortega, NASA Centennial Challenges Program Manager, speaks at a breakfast opening the TouchTomorrow Festival, held in conjunction with the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-10

James Leopore, of team Fetch, from Alexandria, Virginia, speaks with judges as he prepares for the NASA 2014 Sample Return Robot Challenge, Tuesday, June 10, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Team Fetch is one of eighteen teams competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

The team survey robot is seen on the starting platform before begging it's attempt at the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

The Mountaineers team from West Virginia University, watches as their robot attempts the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

The team Survey robot is seen as it conducts a demonstration of the level two challenge at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-12

Team Survey's robot is seen as it conducts a demonstration of the level two challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Thursday, June 12, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

A comparison of water solubility enhancements of organic solutes by aquatic humic materials and commercial humic acids

USGS Publications Warehouse

Chlou, C.T.; Kile, D.E.; Brinton, T.I.; Malcolm, R.L.; Leenheer, J.A.; MacCarthy, P.

1987-01-01

Water solubility enhancements of 1,1-bis(p-chloro-phenyl)-2,2,2-trichloroethane (p,p???-DDT), 2,4,5,2???,5???-pentachlorobiphenyl (2,4,5,2???,5???-PCB), and 2,4,4???-tri-chlorobiphenyl (2,4,4???-PCB) by dissolved organic matter have been studied with the following samples: (1) acidic water samples from the Suwannee River, Georgia, and the Sopchoppy River, Florida; (2) a humic extract of a nearly neutral pH water from the Calcasieu River, Louisiana; (3) commercial humic acids from the Aldrich Chemical Co. and Fluka-Tridom Chemical Corp. The calculated partition coefficients on a dissolved organic carbon basis (Kdoc) for organic solutes with water samples and aquatic humic extracts from this and earlier studies indicate that the enhancement effect varies with the molecular composition of the aquatic humic materials. The Kdoc values with water and aquatic humic samples are, however, far less than the observed Kdoc values obtained with the two commercial samples, by factors of about 4-20. In view of this finding, one should be cautious in interpreting the effects of the dissolved organic matter on solubility enhancement of organic solutes on the basis of the use of commercial humic acids.

Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate

DTIC Science & Technology

2013-02-01

Subsurface Delivery and Distribution of Permanganate February 2013 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for...SUBTITLE Polymer-Enhanced Subsurface Delivery and Distribution of Permanganate 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6...SAMPLING RESULTS ........................................................................................ 28 5.6.1 Permanganate Distribution and Sweep

Engineered pinning landscapes for enhanced 2G coil wire

DOE PAGES

Rupich, Martin W.; Sathyamurthy, Srivatsan; Fleshler, Steven; ...

2016-04-01

We demonstrate a twofold increase in the in-field critical current of AMSC's standard 2G coil wire by irradiation with 18-MeV Au ions. The optimum pinning enhancement is achieved with a dose of 6 × 10 11 Au ions/cm 2. Although the 77 K, self-field critical current is reduced by about 35%, the in-field critical current (H//c) shows a significant enhancement between 4 and 50 K in fields > 1 T. The process was used for the roll-to-roll irradiation of AMSC's standard 46-mm-wide production coated conductor strips, which were further processed into standard copper laminated coil wire. The long-length wires showmore » the same enhancement as attained with short static irradiated samples. The roll-to-roll irradiation process can be incorporated in the standard 2G wire manufacturing, with no modifications to the current process. In conclusion, the enhanced performance of the wire will benefit rotating machine and magnet applications.« less

Moral Enhancement

PubMed Central

Douglas, Thomas

2008-01-01

Opponents of biomedical enhancement often claim that, even if such enhancement would benefit the enhanced, it would harm others. But this objection looks unpersuasive when the enhancement in question is a moral enhancement — an enhancement that will expectably leave the enhanced person with morally better motives than she had previously. In this article I (1) describe one type of psychological alteration that would plausibly qualify as a moral enhancement, (2) argue that we will, in the medium-term future, probably be able to induce such alterations via biomedical intervention, and (3) defend future engagement in such moral enhancements against possible objections. My aim is to present this kind of moral enhancement as a counter-example to the view that biomedical enhancement is always morally impermissible. PMID:19132138

Matrix-enhanced secondary ion mass spectrometry: The Alchemist's solution?

NASA Astrophysics Data System (ADS)

Delcorte, Arnaud

2006-07-01

Because of the requirements of large molecule characterization and high-lateral resolution SIMS imaging, the possibility of improving molecular ion yields by the use of specific sample preparation procedures has recently generated a renewed interest in the static SIMS community. In comparison with polyatomic projectiles, however, signal enhancement by a matrix might appear to some as the alchemist's versus the scientist's solution to the current problems of organic SIMS. In this contribution, I would like to discuss critically the pros and cons of matrix-enhanced SIMS procedures, in the new framework that includes polyatomic ion bombardment. This discussion is based on a short review of the experimental and theoretical developments achieved in the last decade with respect to the three following approaches: (i) blending the analyte with a low-molecular weight organic matrix (MALDI-type preparation procedure); (ii) mixing alkali/noble metal salts with the analyte; (iii) evaporating a noble metal layer on the analyte sample surface (organic molecules, polymers).

The MPLEx Protocol for Multi-omic Analyses of Soil Samples

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

Nicora, Carrie D.; Burnum-Johnson, Kristin E.; Nakayasu, Ernesto S.

Mass spectrometry (MS)-based integrated metaproteomic, metabolomic and lipidomic (multi-omic) studies are transforming our ability to understand and characterize microbial communities in environmental and biological systems. These measurements are even enabling enhanced analyses of complex soil microbial communities, which are the most complex microbial systems known to date. Multi-omic analyses, however, do have sample preparation challenges since separate extractions are typically needed for each omic study, thereby greatly amplifying the preparation time and amount of sample required. To address this limitation, a 3-in-1 method for simultaneous metabolite, protein, and lipid extraction (MPLEx) from the exact same soil sample was created bymore » adapting a solvent-based approach. This MPLEx protocol has proven to be simple yet robust for many sample types and even when utilized for limited quantities of complex soil samples. The MPLEx method also greatly enabled the rapid multi-omic measurements needed to gain a better understanding of the members of each microbial community, while evaluating the changes taking place upon biological and environmental perturbations.« less

Enhanced efficiency of light emitting diodes with a nano-patterned gallium nitride surface realized by soft UV nanoimprint lithography

NASA Astrophysics Data System (ADS)

Zhou, Weimin; Min, Guoquan; Song, Zhitang; Zhang, Jing; Liu, Yanbo; Zhang, Jianping

2010-05-01

This paper reports a significant enhancement in the extraction efficiency of nano-patterned GaN light emitting diodes (LED) realized by soft UV nanoimprint lithography. The 2 inch soft stamp was fabricated using a replication stamp of anodic alumina oxide (AAO) membrane. The light output power was enhanced by 10.9% compared to that of the LED sample without a nano-patterned surface. Up to 41% enhancement in photoluminescence intensity was obtained from the nano-patterned GaN LED sample. The method is simple, cheap and suitable for mass production.

Plasma deposited stability enhancement coating for amorphous ketoprofen.

PubMed

Bosselmann, Stephanie; Owens, Donald E; Kennedy, Rachel L; Herpin, Matthew J; Williams, Robert O

2011-05-01

A hydrophobic fluorocarbon coating deposited onto amorphous ketoprofen via pulsed plasma-enhanced chemical vapor deposition (PPECVD) significantly prolonged the onset of recrystallization compared to uncoated drug. Rapid freezing (RF) employed to produce amorphous ketoprofen was followed by PPECVD of perfluorohexane. The effect of coating thickness on the recrystallization and dissolution behavior of ketoprofen was investigated. Samples were stored in open containers at 40°C and 75% relative humidity, and the onset of recrystallization was monitored by DSC. An increase in coating thickness provided enhanced stability against recrystallization for up to 6 months at accelerated storage conditions (longest time of observation) when compared to three days for uncoated ketoprofen. Results from XPS analysis demonstrated that an increase in coating thickness was associated with improved surface coverage thus enabling superior protection. Dissolution testing showed that at least 80% of ketoprofen was released in buffer pH 6.8 from all coated samples. Overall, an increase in coating thickness resulted in a more complete drug release due to decreased adhesion of the coating to the substrate. Copyright © 2010 Elsevier B.V. All rights reserved.

Polyol-enhanced dispersive liquid-liquid microextraction coupled with gas chromatography and nitrogen phosphorous detection for the determination of organophosphorus pesticides from aqueous samples, fruit juices, and vegetables.

PubMed

Farajzadeh, Mir Ali; Afshar Mogaddam, Mohammad Reza; Alizadeh Nabil, Ali Akbar

2015-12-01

Polyol-enhanced dispersive liquid-liquid microextraction has been proposed for the extraction and preconcentration of some organophosphorus pesticides from different samples. In the present study, a high volume of an aqueous phase containing a polyol (sorbitol) is prepared and then a disperser solvent along with an extraction solvent is rapidly injected into it. Sorbitol showed the best results and it was more effective on the extraction recoveries of the analytes than inorganic salts such as sodium chloride, potassium chloride, and sodium sulfate. Under the optimum extraction conditions, the method showed low limits of detection and quantification within the ranges of 12-56 and 44-162 pg/mL, respectively. Enrichment factors and extraction recoveries were in the ranges of 2799-3033 and 84-92%, respectively. The method precision was evaluated at a concentration of 10 ng/mL of each analyte, and relative standard deviations were found to be less than 5.9% for intraday (n = 6) and less than 7.8% for interday (n = 4). Finally, some aqueous samples were successfully analyzed using the proposed method and four analytes (diazinon, dimethoate, chlorpyrifos, and phosalone) were determined, some of them at ng/mL level. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Application of surface-enhanced Raman spectra to the analysis of Chinese Ephedra soup medicines].

PubMed

Zhang, J; Wang, Y

1998-06-01

A new method was developed to analyse the spectra of ephedrine in Chinese ephedra soup medicines, using surface-enhanced technique to combine thin layer chromatographic (TLC) technique with surface-enhanced Raman spectroscopy (SERS). The study indicates that the main vibrant characteristic spec tral band of the ephedrine molecules can be obtained by TLC in the samples of about 8 microg, and expounds char acteristics of the sample molecules and the silica gel. Therefore, it is clarified that the main chemical composi tion of Chinese medicines can be carried as finger-print type appraisal by combining TLC and SERS.

Tip-enhanced near-field optical microscope with side-on and ATR-mode sample excitation for super-resolution Raman imaging of surfaces

NASA Astrophysics Data System (ADS)

Heilman, A. L.; Gordon, M. J.

2016-06-01

A tip-enhanced near-field optical microscope with side-on and attenuated total reflectance (ATR) excitation and collection is described and used to demonstrate sub-diffraction-limited (super-resolution) optical and chemical characterization of surfaces. ATR illumination is combined with an Au optical antenna tip to show that (i) the tip can quantitatively transduce the optical near-field (evanescent waves) above the surface by scattering photons into the far-field, (ii) the ATR geometry enables excitation and characterization of surface plasmon polaritons (SPPs), whose associated optical fields are shown to enhance Raman scattering from a thin layer of copper phthalocyanine (CuPc), and (iii) SPPs can be used to plasmonically excite the tip for super-resolution chemical imaging of patterned CuPc via tip-enhanced Raman spectroscopy (TERS). ATR-illumination TERS is also quantitatively compared with the more conventional side-on illumination scheme. In both cases, spatial resolution was better than 40 nm and tip on/tip off Raman enhancement factors were >6500. Furthermore, ATR illumination was shown to provide similar Raman signal levels at lower "effective" pump powers due to additional optical energy delivered by SPPs to the active region in the tip-surface gap.

Efficiency enhancement of optimized Latin hypercube sampling strategies: Application to Monte Carlo uncertainty analysis and meta-modeling

NASA Astrophysics Data System (ADS)

Rajabi, Mohammad Mahdi; Ataie-Ashtiani, Behzad; Janssen, Hans

2015-02-01

The majority of literature regarding optimized Latin hypercube sampling (OLHS) is devoted to increasing the efficiency of these sampling strategies through the development of new algorithms based on the combination of innovative space-filling criteria and specialized optimization schemes. However, little attention has been given to the impact of the initial design that is fed into the optimization algorithm, on the efficiency of OLHS strategies. Previous studies, as well as codes developed for OLHS, have relied on one of the following two approaches for the selection of the initial design in OLHS: (1) the use of random points in the hypercube intervals (random LHS), and (2) the use of midpoints in the hypercube intervals (midpoint LHS). Both approaches have been extensively used, but no attempt has been previously made to compare the efficiency and robustness of their resulting sample designs. In this study we compare the two approaches and show that the space-filling characteristics of OLHS designs are sensitive to the initial design that is fed into the optimization algorithm. It is also illustrated that the space-filling characteristics of OLHS designs based on midpoint LHS are significantly better those based on random LHS. The two approaches are compared by incorporating their resulting sample designs in Monte Carlo simulation (MCS) for uncertainty propagation analysis, and then, by employing the sample designs in the selection of the training set for constructing non-intrusive polynomial chaos expansion (NIPCE) meta-models which subsequently replace the original full model in MCSs. The analysis is based on two case studies involving numerical simulation of density dependent flow and solute transport in porous media within the context of seawater intrusion in coastal aquifers. We show that the use of midpoint LHS as the initial design increases the efficiency and robustness of the resulting MCSs and NIPCE meta-models. The study also illustrates that this

Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study.

PubMed

Martínez, Leandro; Malliavin, Thérèse E; Blondel, Arnaud

2011-05-01

The anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two-Mg(2+) binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg(2+) ions. This provides an explanation for the inhibitory effect of high Mg(2+) concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two-step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mechanism, product protonation facilitates dissociation.

New approaches to the analysis of complex samples using fluorescence lifetime techniques and organized media

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

Hertz, P.R.

Fluorescence spectroscopy is a highly sensitive and selective tool for the analysis of complex systems. In order to investigate the efficacy of several steady state and dynamic techniques for the analysis of complex systems, this work focuses on two types of complex, multicomponent samples: petrolatums and coal liquids. It is shown in these studies dynamic, fluorescence lifetime-based measurements provide enhanced discrimination between complex petrolatum samples. Additionally, improved quantitative analysis of multicomponent systems is demonstrated via incorporation of organized media in coal liquid samples. This research provides the first systematic studies of (1) multifrequency phase-resolved fluorescence spectroscopy for dynamic fluorescence spectralmore » fingerprinting of complex samples, and (2) the incorporation of bile salt micellar media to improve accuracy and sensitivity for characterization of complex systems. In the petroleum studies, phase-resolved fluorescence spectroscopy is used to combine spectral and lifetime information through the measurement of phase-resolved fluorescence intensity. The intensity is collected as a function of excitation and emission wavelengths, angular modulation frequency, and detector phase angle. This multidimensional information enhances the ability to distinguish between complex samples with similar spectral characteristics. Examination of the eigenvalues and eigenvectors from factor analysis of phase-resolved and steady state excitation-emission matrices, using chemometric methods of data analysis, confirms that phase-resolved fluorescence techniques offer improved discrimination between complex samples as compared with conventional steady state methods.« less

Dose Enhancement near Metal Interfaces in Synthetic Diamond Based X-ray Dosimeters

NASA Astrophysics Data System (ADS)

Alamoudi, Dalal

Diamond is an attractive material for medical dosimetry due to its radiation hardness, fast response, chemical resilience, small sensitive volume, high spatial resolution, near-tissue equivalence, and energy and dose rate independence. These properties make diamond a promising material for medical dosimetry compared to other semiconductor detector materials and wider radiation detection applications. This study is focused on one of the important factors to consider in the radiation detector; the influence of dose enhancement on the photocurrent performance at metallic interfaces in synthetic diamond radiation dosimeters with carbon based electrodes as a function of bias voltages. Monte Carlo (MC) simulations with BEAMnrc code were carried out to simulate the dose enhancement factor (DEF) and compared against the equivalent photocurrent ratio from experimental investigation. MC simulations show that the sensitive region for the absorbed dose distribution covers a few micrometers distances from the interface. Experimentally, two single crystal (SC) and one polycrystalline (PC) samples with carbon based electrodes were used. The samples were each mounted inside a tissue equivalent encapsulation design in order to minimize fluence perturbations. Copper, Gold and Lead have been investigated experimentally as generators of photoelectrons using 50 kVp and 100 kVp X-rays relevant for medical dosimetry. The results show enhancement in the detectors' photocurrent performance when different metals are butted up to the diamond detector. The variation in the photocurrent ratio measurements depends on the type of diamond samples, their electrode fabrication and the applied bias voltages indicating that the dose enhancement from diamond-metal interface modifies the electronic performance of the detector.

A model-based 'varimax' sampling strategy for a heterogeneous population.

PubMed

Akram, Nuzhat A; Farooqi, Shakeel R

2014-01-01

Sampling strategies are planned to enhance the homogeneity of a sample, hence to minimize confounding errors. A sampling strategy was developed to minimize the variation within population groups. Karachi, the largest urban agglomeration in Pakistan, was used as a model population. Blood groups ABO and Rh factor were determined for 3000 unrelated individuals selected through simple random sampling. Among them five population groups, namely Balochi, Muhajir, Pathan, Punjabi and Sindhi, based on paternal ethnicity were identified. An index was designed to measure the proportion of admixture at parental and grandparental levels. Population models based on index score were proposed. For validation, 175 individuals selected through stratified random sampling were genotyped for the three STR loci CSF1PO, TPOX and TH01. ANOVA showed significant differences across the population groups for blood groups and STR loci distribution. Gene diversity was higher across the sub-population model than in the agglomerated population. At parental level gene diversities are significantly higher across No admixture models than Admixture models. At grandparental level the difference was not significant. A sub-population model with no admixture at parental level was justified for sampling the heterogeneous population of Karachi.

Low illumination color image enhancement based on improved Retinex

NASA Astrophysics Data System (ADS)

Liao, Shujing; Piao, Yan; Li, Bing

2017-11-01

Low illumination color image usually has the characteristics of low brightness, low contrast, detail blur and high salt and pepper noise, which greatly affected the later image recognition and information extraction. Therefore, in view of the degradation of night images, the improved algorithm of traditional Retinex. The specific approach is: First, the original RGB low illumination map is converted to the YUV color space (Y represents brightness, UV represents color), and the Y component is estimated by using the sampling acceleration guidance filter to estimate the background light; Then, the reflection component is calculated by the classical Retinex formula and the brightness enhancement ratio between original and enhanced is calculated. Finally, the color space conversion from YUV to RGB and the feedback enhancement of the UV color component are carried out.

Experimental investigation on variation of physical properties of coal samples subjected to microwave irradiation

NASA Astrophysics Data System (ADS)

Hu, Guozhong; Yang, Nan; Xu, Guang; Xu, Jialin

2018-03-01

The gas drainage rate of low-permeability coal seam is generally less than satisfactory. This leads to the gas disaster of coal mine, and largely restricts the extraction of coalbed methane (CBM), and increases the emission of greenhouse gases in the mining area. Consequently, enhancing the gas drainage rate is an urgent challenge. To solve this problem, a new approach of using microwave irradiation (MWR) as a non-contact physical field excitation method to enhance gas drainage has been attempted. In order to evaluate the feasibility of this method, the methane adsorption, diffusion and penetrability of coal subjected to MWR were experimentally investigated. The variation of methane adsorbed amount, methane diffusion speed and absorption loop for the coal sample before and after MWR were obtained. The findings show that the MWR can change the adsorption property and reduce the methane adsorption capacity of coal. Moreover, the methane diffusion characteristic curves for both the irradiated coal samples and theoriginal coal samples present the same trend. The irradiated coal samples have better methane diffusion ability than the original ones. As the adsorbed methane decreases, the methane diffusion speed increases or remain the same for the sample subjected to MWR. Furthermore, compared to the original coal samples, the area of the absorption loop for irradiated samples increases, especially for the micro-pore and medium-pore stage. This leads to the increase of open pores in the coal, thus improving the gas penetrability of coal. This study provides supports for positive MWR effects on changing the methane adsorption and improving the methane diffusion and the gas penetrability properties of coal samples.

Enhanced photoconductivity by melt quenching method for amorphous organic photorefractive materials

NASA Astrophysics Data System (ADS)

Tsujimura, S.; Fujihara, T.; Sassa, T.; Kinashi, K.; Sakai, W.; Ishibashi, K.; Tsutsumi, N.

2014-10-01

For many optical semiconductor fields of study, the high photoconductivity of amorphous organic semiconductors has strongly been desired, because they make the manufacture of high-performance devices easy when controlling charge carrier transport and trapping is otherwise difficult. This study focuses on the correlation between photoconductivity and bulk state in amorphous organic photorefractive materials to probe the nature of the performance of photoconductivity and to enhance the response time and diffraction efficiency of photorefractivity. The general cooling processes of the quenching method achieved enhanced photoconductivity and a decreased filling rate for shallow traps. Therefore, sample processing, which was quenching in the present case, for photorefractive composites significantly relates to enhanced photorefractivity.

Light absorption enhancement of black carbon from urban haze in Northern China winter.

PubMed

Chen, Bing; Bai, Zhe; Cui, Xinjuan; Chen, Jianmin; Andersson, August; Gustafsson, Örjan

2017-02-01

Atmospheric black carbon (BC) is an important pollutant for both air quality and Earth's energy balance. Estimates of BC climate forcing remain highly uncertain, e.g., due to the mixing with non-absorbing components. Non-absorbing aerosols create a coating on BC and may thereby act as a lens which may enhance the light absorption. However, this absorption enhancement is poorly constrained. To this end a two-step solvent dissolution protocol was employed to remove both organic and inorganic coatings, and then investigate their effects on BC light absorption. Samples were collected at a severely polluted urban area, Jinan, in the North China Plain (NCP) during February 2014. The BC mass absorption cross-section (MAC) was measured for the aerosol samples before and after the solvent-decoating treatment, and the enhancement of MAC (E MAC ) from the coating effect was defined as the ratio. A distinct diurnal pattern for the enhancement was observed, with E MAC 1.3 ± 0.3 (1 S.D.) in the morning, increasing to 2.2 ± 1.0 in the afternoon, after that dropping to 1.5 ± 0.8 in the evening-night. The BC absorption enhancement primarily was associated with urban-scale photochemical production of nitrate and sulfate aerosols. In addition to that, regional-scale haze plume with increasing sulfate levels strengthened the absorption enhancement. These observations offer direct evidence for an increased absorption enhancement of BC due to severe air pollution in China. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Search for Nitrogen-enhanced Metal-poor Stars

NASA Astrophysics Data System (ADS)

Johnson, Jennifer A.; Herwig, Falk; Beers, Timothy C.; Christlieb, Norbert

2007-04-01

Theoretical models of very metal-poor intermediate-mass asymptotic giant branch (AGB) stars predict a large overabundance of primary nitrogen. The very metal-poor, carbon-enhanced, s-process-rich stars, which are thought to be the polluted companions of now extinct AGB stars, provide direct tests of the predictions of these models. Recent studies of the carbon and nitrogen abundances in metal-poor stars have focused on the most carbon-rich stars, leading to a potential selection bias against stars that have been polluted by AGB stars that produced large amounts of nitrogen and hence have small [C/N] ratios. We call these stars nitrogen-enhanced metal-poor (NEMP) stars and define them as having [N/Fe]>+0.5 and [C/N]<-0.5. In this paper we report on the [C/N] abundances of a sample of 21 carbon-enhanced stars, all but three of which have [C/Fe]<+2.0. If NEMP stars were made as easily as carbon-enhanced metal-poor (CEMP) stars, then we expected to find between two and seven NEMP stars. Instead, we found no NEMP stars in our sample. Therefore, this observational bias is not an important contributor to the apparent dearth of N-rich stars. Our [C/N] values are in the same range as values reported previously in the literature (-0.5 to +2.0), and all stars are in disagreement with the predicted [C/N] ratios for both low- and high-mass AGB stars. We suggest that the decrease in [C/N] from the low-mass AGB models is due to enhanced extramixing, while the lack of NEMP stars may be caused by unfavorable mass ratios in binaries or the difficulty of mass transfer in binary systems with large mass ratios. Based on observations obtained at Cerro Tololo Inter-American Observatory and Kitt Peak National Observatory, a division of the National Optical Astronomy Observatory, which is operated by the Association of Universities for Research in Astronomy, Inc., under cooperative agreement with the National Science Foundation.

Enhancing the Assessment of Verbal Aggression through Observational Methodology

ERIC Educational Resources Information Center

van Dulmen, Manfred H. M.; Mata, Andrea D.; Klipfel, Katherine M.

2012-01-01

The assessment of verbal aggression in adolescent and young adult dating relationships has largely relied on self-report methodology. We investigated whether information on verbal aggression derived from an observational assessment would enhance the prediction of romantic relationship satisfaction and dissolution in a sample of young adult dating…

The enhancement in optical and magnetic properties of Na-doped LaFeO3

NASA Astrophysics Data System (ADS)

Devi, E.; Kalaiselvi, B. J.

2018-04-01

La1-xNaxFeO3(x=0.00 and 0.05) were synthesized by sol-gel auto-combustion method. No evidence of impurity phase and the peak (121) slightly shift towards lower angle is confirmed by X-ray diffraction analysis (XRD). The UV-visible spectra show strong absorption peak centered at approximately 231 nm and the calculated optical band gap are found to be 2.73eV, 2.36eV for x = 0.00 and 0.05, respectively. The M-H loop of pure sample is anti-ferromagnetic, whereas those of the Na doped sample shows enhanced ferromagnetic behavior. The remnant magnetization (Mr), saturation magnetization (Ms) and coercive field (Hc) of Na-doped sample are enhanced to 1.06emu/g, 5.39emu/g and 182.84kOe, respectively.

Convolutional neural networks based on augmented training samples for synthetic aperture radar target recognition

NASA Astrophysics Data System (ADS)

Yan, Yue

2018-03-01

A synthetic aperture radar (SAR) automatic target recognition (ATR) method based on the convolutional neural networks (CNN) trained by augmented training samples is proposed. To enhance the robustness of CNN to various extended operating conditions (EOCs), the original training images are used to generate the noisy samples at different signal-to-noise ratios (SNRs), multiresolution representations, and partially occluded images. Then, the generated images together with the original ones are used to train a designed CNN for target recognition. The augmented training samples can contrapuntally improve the robustness of the trained CNN to the covered EOCs, i.e., the noise corruption, resolution variance, and partial occlusion. Moreover, the significantly larger training set effectively enhances the representation capability for other conditions, e.g., the standard operating condition (SOC), as well as the stability of the network. Therefore, better performance can be achieved by the proposed method for SAR ATR. For experimental evaluation, extensive experiments are conducted on the Moving and Stationary Target Acquisition and Recognition dataset under SOC and several typical EOCs.

Comparison of SHOX and associated elements duplications distribution between patients (Lėri-Weill dyschondrosteosis/idiopathic short stature) and population sample.

PubMed

Hirschfeldova, Katerina; Solc, Roman

2017-09-05

The effect of heterozygous duplications of SHOX and associated elements on Lėri-Weill dyschondrosteosis (LWD) and idiopathic short stature (ISS) development is less distinct when compared to reciprocal deletions. The aim of our study was to compare frequency and distribution of duplications within SHOX and associated elements between population sample and LWD (ISS) patients. A preliminary analysis conducted on Czech population sample of 250 individuals compared to our previously reported sample of 352 ISS/LWD Czech patients indicated that rather than the difference in frequency of duplications it is the difference in their distribution. Particularly, there was an increased frequency of duplications residing to the CNE-9 enhancer in our LWD/ISS sample. To see whether the obtained data are consistent across published studies we made a literature survey to get published cases with SHOX or associated elements duplication and formed the merged LWD, the merged ISS, and the merged population samples. Relative frequency of particular region duplication in each of those merged samples were calculated. There was a significant difference in the relative frequency of CNE-9 enhancer duplications (11 vs. 3) and complete SHOX (exon1-6b) duplications (4 vs. 24) (p-value 0.0139 and p-value 0.000014, respectively) between the merged LWD sample and the merged population sample. We thus propose that partial SHOX duplications and small duplications encompassing CNE-9 enhancer could be highly penetrant alleles associated with ISS and LWD development. Copyright © 2017 Elsevier B.V. All rights reserved.

Electrochemical determination of Sudan I in food samples at graphene modified glassy carbon electrode based on the enhancement effect of sodium dodecyl sulphonate.

PubMed

Ma, Xinying; Chao, Mingyong; Wang, Zhaoxia

2013-06-01

This paper describes a novel electrochemical method for the determination of Sudan I in food samples based on the electrochemical catalytic activity of graphene modified glassy carbon electrode (GMGCE) and the enhancement effect of an anionic surfactant: sodium dodecyl sulphonate (SDS). Using pH 6.0 phosphate buffer solution (PBS) as supporting electrolyte and in the presence of 1.5 × 10(-4)mol L(-1) SDS, Sudan I yielded a well-defined and sensitive oxidation peak at a GMGCE. The oxidation peak current of Sudan I remarkably increased in the presence of SDS. The experimental parameters, such as supporting electrolyte, concentration of SDS, and accumulation time, were optimised for Sudan I determination. The oxidation peak current showed a linear relationship with the concentrations of Sudan I in the range of 7.50 × 10(-8)-7.50 × 10(-6)mol L(-1), with the detection limit of 4.0 × 10(-8)mol L(-1). This new voltammetric method was successfully used to determine Sudan I in food products such as ketchup and chili sauce with satisfactory results. Copyright © 2012 Elsevier Ltd. All rights reserved.

Tip-enhanced near-field optical microscope with side-on and ATR-mode sample excitation for super-resolution Raman imaging of surfaces

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

Heilman, A. L.; Gordon, M. J.

A tip-enhanced near-field optical microscope with side-on and attenuated total reflectance (ATR) excitation and collection is described and used to demonstrate sub-diffraction-limited (super-resolution) optical and chemical characterization of surfaces. ATR illumination is combined with an Au optical antenna tip to show that (i) the tip can quantitatively transduce the optical near-field (evanescent waves) above the surface by scattering photons into the far-field, (ii) the ATR geometry enables excitation and characterization of surface plasmon polaritons (SPPs), whose associated optical fields are shown to enhance Raman scattering from a thin layer of copper phthalocyanine (CuPc), and (iii) SPPs can be used tomore » plasmonically excite the tip for super-resolution chemical imaging of patterned CuPc via tip-enhanced Raman spectroscopy (TERS). ATR-illumination TERS is also quantitatively compared with the more conventional side-on illumination scheme. In both cases, spatial resolution was better than 40 nm and tip on/tip off Raman enhancement factors were >6500. Furthermore, ATR illumination was shown to provide similar Raman signal levels at lower “effective” pump powers due to additional optical energy delivered by SPPs to the active region in the tip-surface gap.« less

Transient NOE enhancement in solid-state MAS NMR of mobile systems

NASA Astrophysics Data System (ADS)

Cui, Jiangyu; Li, Jun; Peng, Xinhua; Fu, Riqiang

2017-11-01

It has been known that the heteronuclear cross-relaxation affects the dilute S spin magnetization along the longitudinal direction, causing an overshoot phenomenon for those mobile systems in spin-lattice relaxation rate measurements. Here, we analyze the Solomon equations for an I-S system and derive the transient cross relaxation effect as to when an overshoot phenomenon would take place and what the maximum enhancement could be at the time of the overshoot. In order to utilize such a transient nuclear Overhauser effect (NOE), we first time apply it to dynamic solid samples by inverting the 1H magnetization prior to the excitation of the S spin. It is found that the overshoot depends on the ratio of the I and S spin-lattice relaxation rates, i.e. RSS /RII . When RSS /RII ≫ 1 , the maximum enhancement factor for transient NOE could be larger than that obtained in steady-state NOE experiments. Furthermore, transient NOE appears to be more efficient in terms of sensitivity enhancement of dilute spins in solid-state NMR of mobile systems than the traditional cross polarization scheme whose efficiency is greatly compromised by molecular mobility. A sample of natural abundance L-isoleucine amino acid, in which the spin-lattice relaxation rates for the four methyl carbons are different, has been used to demonstrate sensitivity enhancement factors under various experimental schemes.

Rural Textile Workers Literacy Enhancement Project. Final Performance Report.

ERIC Educational Resources Information Center

Enterprise State Junior Coll., AL.

This document consists of the final report and sample curricula from the Rural Textile Workers Literacy Enhancement Project. The final report details how the project was initiated in April 1993 to help employees of five textile and apparel manufacturing companies in southeastern Alabama improve their literacy and numeracy skills. A second…

Local reconstruction in computed tomography of diffraction enhanced imaging

NASA Astrophysics Data System (ADS)

Huang, Zhi-Feng; Zhang, Li; Kang, Ke-Jun; Chen, Zhi-Qiang; Zhu, Pei-Ping; Yuan, Qing-Xi; Huang, Wan-Xia

2007-07-01

Computed tomography of diffraction enhanced imaging (DEI-CT) based on synchrotron radiation source has extremely high sensitivity of weakly absorbing low-Z samples in medical and biological fields. The authors propose a modified backprojection filtration(BPF)-type algorithm based on PI-line segments to reconstruct region of interest from truncated refraction-angle projection data in DEI-CT. The distribution of refractive index decrement in the sample can be directly estimated from its reconstruction images, which has been proved by experiments at the Beijing Synchrotron Radiation Facility. The algorithm paves the way for local reconstruction of large-size samples by the use of DEI-CT with small field of view based on synchrotron radiation source.

IR sensitivity enhancement of CMOS Image Sensor with diffractive light trapping pixels.

PubMed

Yokogawa, Sozo; Oshiyama, Itaru; Ikeda, Harumi; Ebiko, Yoshiki; Hirano, Tomoyuki; Saito, Suguru; Oinoue, Takashi; Hagimoto, Yoshiya; Iwamoto, Hayato

2017-06-19

We report on the IR sensitivity enhancement of back-illuminated CMOS Image Sensor (BI-CIS) with 2-dimensional diffractive inverted pyramid array structure (IPA) on crystalline silicon (c-Si) and deep trench isolation (DTI). FDTD simulations of semi-infinite thick c-Si having 2D IPAs on its surface whose pitches over 400 nm shows more than 30% improvement of light absorption at λ = 850 nm and the maximum enhancement of 43% with the 540 nm pitch at the wavelength is confirmed. A prototype BI-CIS sample with pixel size of 1.2 μm square containing 400 nm pitch IPAs shows 80% sensitivity enhancement at λ = 850 nm compared to the reference sample with flat surface. This is due to diffraction with the IPA and total reflection at the pixel boundary. The NIR images taken by the demo camera equip with a C-mount lens show 75% sensitivity enhancement in the λ = 700-1200 nm wavelength range with negligible spatial resolution degradation. Light trapping CIS pixel technology promises to improve NIR sensitivity and appears to be applicable to many different image sensor applications including security camera, personal authentication, and range finding Time-of-Flight camera with IR illuminations.

Application of Ultrasound-Assisted Surfactant-Enhanced Emulsification Microextraction Based on Solidification of Floating Organic Droplets and High Performance Liquid Chromatography for Preconcentration and Determination of Alprazolam and Chlordiazepoxide in Human Serum Samples.

PubMed

Goudarzi, Nasser; Amirnavaee, Monavar; Arab Chamjangali, Mansour; Farsimadan, Sahar

2017-07-01

An improved microextraction method is proposed on the basis of ultrasound-assisted surfactant-enhanced emulsification and solidification of a floating organic droplet procedure combined with high performance liquid chromatography for the preconcentration and quantification of alprazolam (ALP) and chlordiazepoxide (CHL) present in a number of human serum samples. Several parameters affecting the extraction efficiency were investigated by the Plackett -Burman factorial design as the screening design. Then the response surface methodology based on the Box-Behnken design was used to optimize the effective parameters in the proposed procedure. The limits of detection for the proposed method were found to be 3.0 and 3.1 ng mL-1 for CHL and ALP, respectively. The calibration curves obtained for the method were linear in the ranges of 10.0-3,500.0 and 10.0-3,000.0 ng mL-1 for CHL and ALP, respectively, with a good determination coefficient. The recoveries of the drugs in the spiked human serum samples were above 93.0%. The developed method was successfully applied to the analysis of these studied drugs in human serum samples. The pre-treatment of the serum samples was performed using acetonitrile to remove the proteins. The proposed procedure was an accurate and reliable one for the determination and preconcentration of these drugs in blood samples. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Toward Monitoring Parkinson's Through Analysis of Static Handwriting Samples: A Quantitative Analytical Framework.

PubMed

Zhi, Naiqian; Jaeger, Beverly Kris; Gouldstone, Andrew; Sipahi, Rifat; Frank, Samuel

2017-03-01

Detection of changes in micrographia as a manifestation of symptomatic progression or therapeutic response in Parkinson's disease (PD) is challenging as such changes can be subtle. A computerized toolkit based on quantitative analysis of handwriting samples would be valuable as it could supplement and support clinical assessments, help monitor micrographia, and link it to PD. Such a toolkit would be especially useful if it could detect subtle yet relevant changes in handwriting morphology, thus enhancing resolution of the detection procedure. This would be made possible by developing a set of metrics sensitive enough to detect and discern micrographia with specificity. Several metrics that are sensitive to the characteristics of micrographia were developed, with minimal sensitivity to confounding handwriting artifacts. These metrics capture character size-reduction, ink utilization, and pixel density within a writing sample from left to right. They are used here to "score" handwritten signatures of 12 different individuals corresponding to healthy and symptomatic PD conditions, and sample control signatures that had been artificially reduced in size for comparison purposes. Moreover, metric analyses of samples from ten of the 12 individuals for which clinical diagnosis time is known show considerable informative variations when applied to static signature samples obtained before and after diagnosis. In particular, a measure called pixel density variation showed statistically significant differences ( ) between two comparison groups of remote signature recordings: earlier versus recent, based on independent and paired t-test analyses on a total of 40 signature samples. The quantitative framework developed here has the potential to be used in future controlled experiments to study micrographia and links to PD from various aspects, including monitoring and assessment of applied interventions and treatments. The inherent value in this methodology is further enhanced by

Particle shape analysis of volcanic clast samples with the Matlab tool MORPHEO

NASA Astrophysics Data System (ADS)

Charpentier, Isabelle; Sarocchi, Damiano; Rodriguez Sedano, Luis Angel

2013-02-01

This paper presents a modular Matlab tool, namely MORPHEO, devoted to the study of particle morphology by Fourier analysis. A benchmark made of four sample images with different features (digitized coins, a pebble chart, gears, digitized volcanic clasts) is then proposed to assess the abilities of the software. Attention is brought to the Weibull distribution introduced to enhance fine variations of particle morphology. Finally, as an example, samples pertaining to a lahar deposit located in La Lumbre ravine (Colima Volcano, Mexico) are analysed. MORPHEO and the benchmark are freely available for research purposes.

Sampling hazelnuts for aflatoxin: uncertainty associated with sampling, sample preparation, and analysis.

PubMed

Ozay, Guner; Seyhan, Ferda; Yilmaz, Aysun; Whitaker, Thomas B; Slate, Andrew B; Giesbrecht, Francis

2006-01-01

The variability associated with the aflatoxin test procedure used to estimate aflatoxin levels in bulk shipments of hazelnuts was investigated. Sixteen 10 kg samples of shelled hazelnuts were taken from each of 20 lots that were suspected of aflatoxin contamination. The total variance associated with testing shelled hazelnuts was estimated and partitioned into sampling, sample preparation, and analytical variance components. Each variance component increased as aflatoxin concentration (either B1 or total) increased. With the use of regression analysis, mathematical expressions were developed to model the relationship between aflatoxin concentration and the total, sampling, sample preparation, and analytical variances. The expressions for these relationships were used to estimate the variance for any sample size, subsample size, and number of analyses for a specific aflatoxin concentration. The sampling, sample preparation, and analytical variances associated with estimating aflatoxin in a hazelnut lot at a total aflatoxin level of 10 ng/g and using a 10 kg sample, a 50 g subsample, dry comminution with a Robot Coupe mill, and a high-performance liquid chromatographic analytical method are 174.40, 0.74, and 0.27, respectively. The sampling, sample preparation, and analytical steps of the aflatoxin test procedure accounted for 99.4, 0.4, and 0.2% of the total variability, respectively.

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

Team AERO, from the Worcester Polytechnic Institute (WPI) transports their robot to the competition field for the level one of the competition during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-11

Robots that will be competing in the Level one competition are seen as they sit in impound prior to the start of competition at the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Wednesday, June 11, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library

2014-06-14

Ahti Heinla, left, and Sulo Kallas, right, from Estonia, prepare team KuuKulgur's robot for the rerun of the level one challenge during the 2014 NASA Centennial Challenges Sample Return Robot Challenge, Saturday, June 14, 2014, at the Worcester Polytechnic Institute (WPI) in Worcester, Mass. Eighteen teams are competing for a $1.5 million NASA prize purse. Teams will be required to demonstrate autonomous robots that can locate and collect samples from a wide and varied terrain, operating without human control. The objective of this NASA-WPI Centennial Challenge is to encourage innovations in autonomous navigation and robotics technologies. Innovations stemming from the challenge may improve NASA's capability to explore a variety of destinations in space, as well as enhance the nation's robotic technology for use in industries and applications on Earth. Photo Credit: (NASA/Joel Kowsky)

2014 NASA Centennial Challenges Sample Return Robot Challenge

NASA Image and Video Library