WorldWideScience

Sample records for biomolecular systems determinants

  1. Improvements in continuum modeling for biomolecular systems

    CERN Document Server

    Qiao, Yu

    2015-01-01

    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulation. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.

  2. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  3. Improvements in continuum modeling for biomolecular systems

    Science.gov (United States)

    Yu, Qiao; Ben-Zhuo, Lu

    2016-01-01

    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress. Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

  4. Biomolecular computing systems: principles, progress and potential.

    Science.gov (United States)

    Benenson, Yaakov

    2012-06-12

    The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.

  5. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.

    2007-01-01

    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation method

  6. Quantum dynamics of bio-molecular systems in noisy environments

    OpenAIRE

    Huelga S.F.; Plenio M.B.

    2012-01-01

    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...

  7. Retroactivity in the Context of Modularly Structured Biomolecular Systems

    Science.gov (United States)

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos

    2015-01-01

    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular. PMID:26137457

  8. Quantum dynamics of bio-molecular systems in noisy environments

    CERN Document Server

    Plenio, M B

    2012-01-01

    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.

  9. Engineering intracellular active transport systems as in vivo biomolecular tools.

    Energy Technology Data Exchange (ETDEWEB)

    Bachand, George David; Carroll-Portillo, Amanda

    2006-11-01

    Active transport systems provide essential functions in terms of cell physiology and metastasis. These systems, however, are also co-opted by invading viruses, enabling directed transport of the virus to and from the cell's nucleus (i.e., the site of virus replication). Based on this concept, fundamentally new approaches for interrogating and manipulating the inner workings of living cells may be achievable by co-opting Nature's active transport systems as an in vivo biomolecular tool. The overall goal of this project was to investigate the ability to engineer kinesin-based transport systems for in vivo applications, specifically the collection of effector proteins (e.g., transcriptional regulators) within single cells. In the first part of this project, a chimeric fusion protein consisting of kinesin and a single chain variable fragment (scFv) of an antibody was successfully produced through a recombinant expression system. The kinesin-scFv retained both catalytic and antigenic functionality, enabling selective capture and transport of target antigens. The incorporation of a rabbit IgG-specific scFv into the kinesin established a generalized system for functionalizing kinesin with a wide range of target-selective antibodies raised in rabbits. The second objective was to develop methods of isolating the intact microtubule network from live cells as a platform for evaluating kinesin-based transport within the cytoskeletal architecture of a cell. Successful isolation of intact microtubule networks from two distinct cell types was demonstrated using glutaraldehyde and methanol fixation methods. This work provides a platform for inferring the ability of kinesin-scFv to function in vivo, and may also serve as a three-dimensional scaffold for evaluating and exploiting kinesin-based transport for nanotechnological applications. Overall, the technology developed in this project represents a first-step in engineering active transport system for in vivo

  10. In situ monitoring of biomolecular processes in living systems using surface-enhanced Raman scattering

    Science.gov (United States)

    Altunbek, Mine; Kelestemur, Seda; Culha, Mustafa

    2015-12-01

    Surface-enhanced Raman scattering (SERS) continues to strive to gather molecular level information from dynamic biological systems. It is our ongoing effort to utilize the technique for understanding of the biomolecular processes in living systems such as eukaryotic and prokaryotic cells. In this study, the technique is investigated to identify cell death mechanisms in 2D and 3D in vitro cell culture models, which is a very important process in tissue engineering and pharmaceutical applications. Second, in situ biofilm formation monitoring is investigated to understand how microorganisms respond to the environmental stimuli, which inferred information can be used to interfere with biofilm formation and fight against their pathogenic activity.

  11. Formaldehyde—A Key Monad of the Biomolecular System

    Directory of Open Access Journals (Sweden)

    Bodo Lachmann

    2013-08-01

    Full Text Available Experiments will be presented and reviewed to support the hypothesis that the intrinsic reactivity of formaldehyde may lead to the formation of a rather comprehensive set of defined biomolecules, including D-glucose, thus fostering concepts of evolution considering the existence of a premetabolic system as a primordial step in the generation of life.

  12. Fundamental behavior of a model biomolecular amphiphile system

    Science.gov (United States)

    Haverstick, Kraig Leonard

    An interest in the fundamental interactions between protein components, in the form of either single amino acids or peptides, unifies the work represented in this thesis. These fundamental interactions drive protein folding, enzyme-substrate binding, and cell adhesion to extracellular ligands. The technology of lipidation was used to isolate these protein interactions. Lipidation of a water-soluble amino acid or peptide sequence confined the protein component to the air-water interface or to a self-assembled structure in water. Compression of the molecules at the air-water interface ordered them into a solid-like monolayer, and Langmuir-Blodgett deposition produced a surface modification with protein component presented in a controlled, orderly manner. These molecules have potential applications as biomaterials coatings or drug delivery devices. A method for determination of specific hydrogen bonding interactions through cocrystallization of two complementary peptide sequences is also described. In order to understand the effect of lipidation and lipid structure on peptide behavior, a comprehensive study of tail designs was first undertaken. Tail length, linkage group, linker, spacer length, and headgroup chirality, orientation, and terminal group were systematically varied in simple amino acid amphiphiles. Monolayer assembly, thermal stability, and structure were studied with Langmuir isotherms and Fourier transform infrared spectroscopy. Each part of the tail structure was found to affect monolayer behavior. With lipid effects better understood, peptide amphiphiles were designed, synthesized, and studied using peptide sequences of importance for cell adhesion. The sequences [IV-H1] from type IV collagen and Arg-Gly-Asp (RGD) were lipidated and characterized in monolayers by Langmuir isotherms and Fourier transform infrared spectroscopy. Biological functionality was determined by melanoma cell spreading assays. Peptide presentation was found to be critical for

  13. Optical sensing systems based on biomolecular recognition of recombinant proteins

    Science.gov (United States)

    Salins, Lyndon L.; Schauer-Vukasinovic, Vesna; Daunert, Sylvia

    1998-05-01

    SIte-directed mutagenesis and the associated site-specific fluorescent labeling of proteins can be used to rationally design reagentless fluorescent molecular senors. The phosphate binding protein (PBP) and calmodulin (CaM) bind to phosphate and calcium in a highly specific manner. These ions induce a hinge motion in the proteins, and the resultant conformational change constitutes the basis of the sensor development. By labeling each protein at a specific site with environment-sensitive fluorescent probes, these conformational changes can be monitored and related to the amount of analyte ion present. In this study, the polymerase chain reaction was used to construct mutants of PBP and CaM that have a single cysteine at positions 197 and 109, respectively. Each protein was site-specifically labeled through the sulfhydryl group of the introduced cysteine residue at a single location with an environment-sensitive fluorescent probe. Characterization of the steady-state fluorescence indicated an enhancement of signal intensity upon binding of the analyte ion. Highly sensitive and selective and selective sensing systems for phosphate and calcium were obtained by using this approach.

  14. Nonlocal Dynamics in Nonlinear Biomolecular and Optical Systems

    DEFF Research Database (Denmark)

    Larsen, Peter Ulrik Vingaard

    2006-01-01

    Begrebet ikke-lokalitet nyder større og større interesse indenfor modelleringen af fysiske systemer - og med god grund. At en model er ikke-lokal betyder at for at kunne beskrive dens fysiske egenskaber i et givet punkt korrekt er det ikke tilstrækkeligt blot at betragte omstændighederne netop...... model af et DNA-molekyle og en af en ikke-linæer optisk krystal - i en ikke-lokal sammenhæng. I levende celler er det umådeligt vigtige DNA-molekyle ansvarlig for fremstilling af proteiner og celledeling. Begge disse aktiviteter kræver en åbning af molekylets to strenge og for at muliggøre dette antages...... det at energilokalisering spiller en væsentlig rolle. Det er velkendt at introducerede inhomogeniteter på en model af molekyl-kæden - disse kan tænkes at simulere effekten af enzymer - kan lokalisere vibrationsenergi og dermed muliggøre åbning af DNA. I dette arbejde har vi udvidet en anerkendt model...

  15. fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems.

    Science.gov (United States)

    Mendieta-Moreno, Jesús I; Walker, Ross C; Lewis, James P; Gómez-Puertas, Paulino; Mendieta, Jesús; Ortega, José

    2014-05-13

    In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (fireball) with the amber force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.

  16. Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology

    Science.gov (United States)

    Lee, Younghee; Li, Jianrong; Gamazon, Eric; Chen, James L.; Tikhomirov, Anna; Cox, Nancy J.; Lussier, Yves A.

    2010-01-01

    A key challenge for genome-wide association studies (GWAS) is to understand how single nucleotide polymorphisms (SNPs) mechanistically underpin complex diseases. While this challenge has been addressed partially by Gene Ontology (GO) enrichment of large list of host genes of SNPs prioritized in GWAS, these enrichment have not been formally evaluated. Here, we develop a novel computational approach anchored in information theoretic similarity, by systematically mining lists of host genes of SNPs prioritized in three adult-onset diabetes mellitus GWAS. The “gold-standard” is based on GO associated with 20 published diabetes SNPs’ host genes and on our own evaluation. We computationally identify 69 similarity-predicted GO independently validated in all three GWAS (FDR<5%), enriched with those of the gold-standard (odds ratio=5.89, P=4.81e-05), and these terms can be organized by similarity criteria into 11 groupings termed “biomolecular systems”. Six biomolecular systems were corroborated by the gold-standard and the remaining five were previously uncharacterized. http://lussierlab.org/publications/ITS-GWAS PMID:21347143

  17. Towards local electromechanical probing of cellular and biomolecular systems in a liquid environment

    Energy Technology Data Exchange (ETDEWEB)

    Kalinin, Sergei V [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Rodriguez, Brian J [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Jesse, Stephen [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Seal, Katyayani [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Proksch, Roger [Asylum Research, Santa Barbara, CA 93117 (United States); Hohlbauch, Sophia [Asylum Research, Santa Barbara, CA 93117 (United States); Revenko, Irene [Asylum Research, Santa Barbara, CA 93117 (United States); Thompson, Gary Lee [Department of Bioengineering, Clemson University, Clemson, SC 29634 (United States); Vertegel, Alexey A [Department of Bioengineering, Clemson University, Clemson, SC 29634 (United States)

    2007-10-24

    Electromechanical coupling is ubiquitous in biological systems, with examples ranging from simple piezoelectricity in calcified and connective tissues to voltage-gated ion channels, energy storage in mitochondria, and electromechanical activity in cardiac myocytes and outer hair cell stereocilia. Piezoresponse force microscopy (PFM) originally emerged as a technique to study electromechanical phenomena in ferroelectric materials, and in recent years has been employed to study a broad range of non-ferroelectric polar materials, including piezoelectric biomaterials. At the same time, the technique has been extended from ambient to liquid imaging on model ferroelectric systems. Here, we present results on local electromechanical probing of several model cellular and biomolecular systems, including insulin and lysozyme amyloid fibrils, breast adenocarcinoma cells, and bacteriorhodopsin in a liquid environment. The specific features of PFM operation in liquid are delineated and bottlenecks on the route towards nanometre-resolution electromechanical imaging of biological systems are identified.

  18. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, G.; Garcia, A.E. [Los Alamos National Lab., NM (United States). Theoretical Biology and Biophysics Group; Soumpasis, D.M. [Max-Planck-Inst for Biophysical Chemistry, Goettingen (Germany). Biocomputation Group

    1994-10-01

    To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems. The potential-of-mean-force (PMF) formalism attempts to describe quantitatively the interactions of the solvent with biological macromolecules on the basis of an approximate statistical-mechanical representation. At its current status of development, it deals with ionic effects on the biomolecular structure and with the structural hydration of biomolecules. The underlying idea of the PMF formalism is to identify the dominant sources of interactions and incorporate these interactions into the theoretical formalism using PMF`s (or particle correlation functions) extracted from bulk-liquid systems. In the following, the authors shall briefly outline the statistical-mechanical foundation of the PMF formalism and introduce the PMF expansion formalism, which is intimately linked to superposition approximations for higher-order particle correlation functions. The authors shall then sketch applications, which describe the effects of the ionic environment on nucleic-acid structure. Finally, the authors shall present the more recent extension of the PMF idea to describe quantitatively the structural hydration of biomolecules. Results for the interface of ice and water and for the hydration of deoxyribonucleic acid (DNA) will be discussed.

  19. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems

    Science.gov (United States)

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew

    2013-11-01

    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of the fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at http://lsec.cc.ac.cn/~lubz/afmpb.html and a mirror site at http://mccammon.ucsd.edu/. This paper is a brief summary of the program: the algorithms, the implementation and the usage. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check http://lsec.cc.ac.cn/lubz/afmpb.html for updates and changes. Running time: The running time varies with the number of discretized elements (N) in the system and their distributions. In most cases, it scales linearly as a function of N.

  20. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems.

    Science.gov (United States)

    Moradi, Mahmoud; Tajkhorshid, Emad

    2014-07-01

    Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach.

  1. PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems.

    Science.gov (United States)

    Torras, Juan; Roberts, Benjamin P; Seabra, Gustavo M; Trickey, Samuel B

    2015-01-01

    PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.

  2. Variational Methods for Biomolecular Modeling

    CERN Document Server

    Wei, Guo-Wei

    2016-01-01

    Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrosta...

  3. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications.

    Science.gov (United States)

    Verma, Arjun; Fratto, Brian E; Privman, Vladimir; Katz, Evgeny

    2016-07-05

    We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  4. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications

    Directory of Open Access Journals (Sweden)

    Arjun Verma

    2016-07-01

    Full Text Available We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  5. Diffusion Monte Carlo applied to weak interactions - hydrogen bonding and aromatic stacking in (bio-)molecular model systems

    Science.gov (United States)

    Fuchs, M.; Ireta, J.; Scheffler, M.; Filippi, C.

    2006-03-01

    Dispersion (Van der Waals) forces are important in many molecular phenomena such as self-assembly of molecular crystals or peptide folding. Calculating this nonlocal correlation effect requires accurate electronic structure methods. Usual density-functional theory with generalized gradient functionals (GGA-DFT) fails unless empirical corrections are added that still need extensive validation. Quantum chemical methods like MP2 and coupled cluster are more accurate, yet limited to rather small systems by their unfavorable computational scaling. Diffusion Monte Carlo (DMC) can provide accurate molecular total energies and remains feasible also for larger systems. Here we apply the fixed-node DMC method to (bio-)molecular model systems where dispersion forces are significant: (dimethyl-) formamide and benzene dimers, and adenine-thymine DNA base pairs. Our DMC binding energies agree well with data from coupled cluster (CCSD(T)), in particular for stacked geometries where GGA-DFT fails qualitatively and MP2 predicts too strong binding.

  6. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond

    2008-01-01

    Comprehensive, Up-to-Date Coverage of Spectroscopy Theory and its Applications to Biological SystemsAlthough a multitude of books have been published about spectroscopy, most of them only occasionally refer to biological systems and the specific problems of biomolecular EPR (bioEPR). Biomolecular EPR Spectroscopy provides a practical introduction to bioEPR and demonstrates how this remarkable tool allows researchers to delve into the structural, functional, and analytical analysis of paramagnetic molecules found in the biochemistry of all species on the planet. A Must-Have Reference in an Intrinsically Multidisciplinary FieldThis authoritative reference seamlessly covers all important bioEPR applications, including low-spin and high-spin metalloproteins, spin traps and spin lables, interaction between active sites, and redox systems. It is loaded with practical tricks as well as do's and don'ts that are based on the author's 30 years of experience in the field. The book also comes with an unprecedented set of...

  7. Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

    Science.gov (United States)

    Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

    2015-04-14

    We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

  8. PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems.

    Science.gov (United States)

    Fleck, Markus; Polyansky, Anton A; Zagrovic, Bojan

    2016-04-12

    Accurate estimation of configurational entropy from the in silico-generated biomolecular ensembles, e.g., from molecular dynamics (MD) trajectories, is dependent strongly on exhaustive sampling for physical reasons. This, however, creates a major computational problem for the subsequent estimation of configurational entropy using the Maximum Information Spanning Tree (MIST) or Mutual Information Expansion (MIE) approaches for internal molecular coordinates. In particular, the available software for such estimation exhibits serious limitations when it comes to molecules with hundreds or thousands of atoms, because of its reliance on a serial program architecture. To overcome this problem, we have developed a parallel, hybrid MPI/openMP C++ implementation of MIST and MIE, called PARENT, which is particularly optimized for high-performance computing and provides efficient estimation of configurational entropy in different biological processes (e.g., protein-protein interactions). In addition, PARENT also allows for a detailed mapping of intramolecular allosteric networks. Here, we benchmark the program on a set of 1-μs-long MD trajectories of 10 different protein complexes and their components, demonstrating robustness and good scalability. A direct comparison between MIST and MIE on the same dataset demonstrates a superior convergence behavior for the former approach, when it comes to total simulation length and configurational-space binning.

  9. Constructing Surrogate Models of Complex Systems with Enhanced Sparsity: Quantifying the influence of conformational uncertainty in biomolecular solvation

    Energy Technology Data Exchange (ETDEWEB)

    Lei, Huan; Yang, Xiu; Zheng, Bin; Baker, Nathan A.

    2015-11-05

    Biomolecules exhibit conformational fluctuations near equilibrium states, inducing uncertainty in various biological properties in a dynamic way. We have developed a general method to quantify the uncertainty of target properties induced by conformational fluctuations. Using a generalized polynomial chaos (gPC) expansion, we construct a surrogate model of the target property with respect to varying conformational states. We also propose a method to increase the sparsity of the gPC expansion by defining a set of conformational “active space” random variables. With the increased sparsity, we employ the compressive sensing method to accurately construct the surrogate model. We demonstrate the performance of the surrogate model by evaluating fluctuation-induced uncertainty in solvent-accessible surface area for the bovine trypsin inhibitor protein system and show that the new approach offers more accurate statistical information than standard Monte Carlo approaches. Further more, the constructed surrogate model also enables us to directly evaluate the target property under various conformational states, yielding a more accurate response surface than standard sparse grid collocation methods. In particular, the new method provides higher accuracy in high-dimensional systems, such as biomolecules, where sparse grid performance is limited by the accuracy of the computed quantity of interest. Our new framework is generalizable and can be used to investigate the uncertainty of a wide variety of target properties in biomolecular systems.

  10. PREFACE: 1st Nano-IBCT Conference 2011 - Radiation Damage of Biomolecular Systems: Nanoscale Insights into Ion Beam Cancer Therapy

    Science.gov (United States)

    Huber, Bernd A.; Malot, Christiane; Domaracka, Alicja; Solov'yov, Andrey V.

    2012-07-01

    The 1st Nano-IBCT Conference entitled 'Radiation Damage in Biomolecular Systems: Nanoscale Insights into Ion Beam Cancer Therapy' was held in Caen, France, in October 2011. The Meeting was organised in the framework of the COST Action MP1002 (Nano-IBCT) which was launched in December 2010 (http://fias.uni-frankfurt.de/nano-ibct). This action aims to promote the understanding of mechanisms and processes underlying the radiation damage of biomolecular systems at the molecular and nanoscopic level and to use the findings to improve the strategy of Ion Beam Cancer Therapy. In the hope of achieving this, participants from different disciplines were invited to represent the fields of physics, biology, medicine and chemistry, and also included those from industry and the operators of hadron therapy centres. Ion beam therapy offers the possibility of excellent dose localization for treatment of malignant tumours, minimizing radiation damage in normal healthy tissue, while maximizing cell killing within the tumour. Several ion beam cancer therapy clinical centres are now operating in Europe and elsewhere. However, the full potential of such therapy can only be exploited by better understanding the physical, chemical and biological mechanisms that lead to cell death under ion irradiation. Considering a range of spatio-temporal scales, the proposed action therefore aims to combine the unique experimental and theoretical expertise available within Europe to acquire greater insight at the nanoscopic and molecular level into radiation damage induced by ion impact. Success in this endeavour will be both an important scientific breakthrough and give great impetus to the practical improvement of this innovative therapeutic technique. Ion therapy potentially provides an important advance in cancer therapy and the COST action MP1002 will be very significant in ensuring Europe's leadership in this field, providing the scientific background, required data and mechanistic insight which

  11. Open-ended response theory with polarizable embedding: multiphoton absorption in biomolecular systems.

    Science.gov (United States)

    Steindal, Arnfinn Hykkerud; Beerepoot, Maarten T P; Ringholm, Magnus; List, Nanna Holmgaard; Ruud, Kenneth; Kongsted, Jacob; Olsen, Jógvan Magnus Haugaard

    2016-10-12

    We present the theory and implementation of an open-ended framework for electric response properties at the level of Hartree-Fock and Kohn-Sham density functional theory that includes effects from the molecular environment modeled by the polarizable embedding (PE) model. With this new state-of-the-art multiscale functionality, electric response properties to any order can be calculated for molecules embedded in polarizable atomistic molecular environments ranging from solvents to complex heterogeneous macromolecules such as proteins. In addition, environmental effects on multiphoton absorption (MPA) properties can be studied by evaluating single residues of the response functions. The PE approach includes mutual polarization effects between the quantum and classical parts of the system through induced dipoles that are determined self-consistently with respect to the electronic density. The applicability of our approach is demonstrated by calculating MPA strengths up to four-photon absorption for the green fluorescent protein. We show how the size of the quantum region, as well as the treatment of the border between the quantum and classical regions, is crucial in order to obtain reliable MPA predictions.

  12. FLOSYS--a web-accessible workflow system for protocol-driven biomolecular sequence analysis.

    Science.gov (United States)

    Badidi, E; Lang, B F; Burger, G

    2004-11-01

    FLOSYS is an interactive web-accessible bioinformatics workflow system designed to assist biologists in multi-step data analyses. FLOSYS allows the user to create complex analysis pathways (protocols) graphically, similar to drawing a flowchart: icons representing particular bioinformatics tools are dragged and dropped onto a canvas and lines connecting those icons are drawn to specify the relationships between the tools. In addition, FLOSYS permits to select input-data, execute the protocol and store the results in a personal workspace. The three-tier architecture of FLOSYS has been implemented in Java and uses a relational database system together with new technologies for distributed and web computing such as CORBA, RMI, JSP and JDBC. The prototype of FLOSYS, which is part of the bioinformatics workbench AnaBench, is accessible on-line at http://malawimonas.bcm.umontreal.ca: 8091/anabench. The entire package is available on request to academic groups who wish to have a customized local analysis environment for research or teaching.

  13. Attofarad resolution potentiostat for electrochemical measurements on nanoscale biomolecular interfacial systems

    Science.gov (United States)

    Carminati, Marco; Ferrari, Giorgio; Sampietro, Marco

    2009-12-01

    We present an instrument that enables electrochemical measurements (cyclic voltammetry, impedance tracking, and impedance spectroscopy) on submicrometric samples. The system features a frequency range from dc to 1 MHz and a current resolution of 10 fA for a measurement time of 1 s, giving a sensitivity of few attofarads in terms of measurable capacitance with an applied voltage of only 100 mV. These performances are obtained using a low-noise wide-bandwidth integrator/differentiator stage to sense the input current and a modular approach to minimize the effect of input stray capacitances. A digitally implemented lock-in filter optimally extracts the impedance of the sample, providing time tracking and spectroscopy operating modes. This computer-based and flexible instrument is well suited for characterizing and tracking the electrical properties of biomolecules kept in the physiological solution down to the nanoscale.

  14. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicu...

  15. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.

    Science.gov (United States)

    Vreede, Jocelyne; Wolf, Maarten G; de Leeuw, Simon W; Bolhuis, Peter G

    2009-05-07

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in an alternating way significantly accelerates the folding process (Wolf, M. G.; de Leeuw, S. W. Biophys. J. 2008, 94, 3742). As the biasing potentials are only active during a fixed time interval, this alternating scheme does not represent a thermodynamic equilibrium. In this work, we present a Hamiltonian replica exchange molecular dynamics (REMD) scheme that aims to shuffle and reorder hydrogen bonds in the protein backbone. We therefore apply adapted hydrogen bond potentials in a Hamiltonian REMD scheme, which we call hydrogen bond switching (HS). To compare the performance of the HS to a standard REMD method, we performed HS and temperature REMD simulations of a beta-heptapeptide in methanol. Both methods sample the conformational space to a similar extent. As the HS simulation required only five replicas, while the REMD simulation required 20 replicas, the HS method is significantly more efficient. We tested the HS method also on a larger system, 16-residue polyalanine in water. Both of the simulations starting from a completely unfolded and a folded conformation resulted in an ensemble with, apart from the starting structure, similar conformational minima. We can conclude that the HS method provides an efficient way to sample the conformational space of a protein, without requiring knowledge of the folded states beforehand. In addition, these simulations revealed that convergence was hampered by replicas having a preference for specific biasing potentials. As this sorting effect is inherent to any Hamiltonian REMD method, finding a solution will result in an additional increase in the efficiency of Hamiltonian REMD methods in general.

  16. Integrative NMR for biomolecular research.

    Science.gov (United States)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R; Tonelli, Marco; Westler, William M; Butcher, Samuel E; Henzler-Wildman, Katherine A; Markley, John L

    2016-04-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html ).

  17. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2010-01-01

    executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new “hardware” is not needed to solve new problems; and (last but not least) it is Turing complete......Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...

  18. Programming in Biomolecular Computation

    DEFF Research Database (Denmark)

    Hartmann, Lars; Jones, Neil; Simonsen, Jakob Grue

    2010-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...... in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level....

  19. Biomolecular electrostatics and solvation: a computational perspective.

    Science.gov (United States)

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

    2012-11-01

    An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

  20. Grid computing and biomolecular simulation.

    Science.gov (United States)

    Woods, Christopher J; Ng, Muan Hong; Johnston, Steven; Murdock, Stuart E; Wu, Bing; Tai, Kaihsu; Fangohr, Hans; Jeffreys, Paul; Cox, Simon; Frey, Jeremy G; Sansom, Mark S P; Essex, Jonathan W

    2005-08-15

    Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

  1. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang

    2013-07-01

    Full Text Available This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications.

  2. Nanoarchitectonics of biomolecular assemblies for functional applications

    Science.gov (United States)

    Avinash, M. B.; Govindaraju, T.

    2014-10-01

    The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.

  3. Genetically designed biomolecular capping system for mesoporous silica nanoparticles enables receptor-mediated cell uptake and controlled drug release

    CERN Document Server

    Datz, Stefan; Gattner, Michael; Weiss, Veronika; Brunner, Korbinian; Bretzler, Johanna; von Schirnding, Constantin; Spada, Fabio; Engelke, Hanna; Vrabel, Milan; Bräuchle, Christoph; Carell, Thomas; Bein, Thomas

    2015-01-01

    Effective and controlled drug delivery systems with on-demand release and targeting abilities have received enormous attention for biomedical applications. Here, we describe a novel enzyme-based cap system for mesoporous silica nanoparticles (MSNs) that is directly combined with a targeting ligand via bio-orthogonal click chemistry. The capping system is based on the pH-responsive binding of an aryl-sulfonamide-functionalized MSN and the enzyme carbonic anhydrase (CA). An unnatural amino acid (UAA) containing a norbornene moiety was genetically incorporated into CA. This UAA allowed for the site-specific bio-orthogonal attachment of even very sensitive targeting ligands such as folic acid and anandamide. This leads to specific receptor-mediated cell and stem cell uptake. We demonstrate the successful delivery and release of the chemotherapeutic agent Actinomycin D to KB cells. This novel nanocarrier concept provides a promising platform for the development of precisely controllable and highly modular theranos...

  4. Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems.

    Science.gov (United States)

    Bromley, Elizabeth H C; Channon, Kevin; Moutevelis, Efrosini; Woolfson, Derek N

    2008-01-18

    There are several approaches to creating synthetic-biological systems. Here, we describe a molecular-design approach. First, we lay out a possible synthetic-biology space, which we define with a plot of complexity of components versus divergence from nature. In this scheme, there are basic units, which range from natural amino acids to totally synthetic small molecules. These are linked together to form programmable tectons, for example, amphipathic alpha-helices. In turn, tectons can interact to give self-assembled units, which can combine and organize further to produce functional assemblies and systems. To illustrate one path through this vast landscape, we focus on protein engineering and design. We describe how, for certain protein-folding motifs, polypeptide chains can be instructed to fold. These folds can be combined to give structured complexes, and function can be incorporated through computational design. Finally, we describe how protein-based systems may be encapsulated to control and investigate their functions.

  5. Genetically designed biomolecular capping system for mesoporous silica nanoparticles enables receptor-mediated cell uptake and controlled drug release

    Science.gov (United States)

    Datz, Stefan; Argyo, Christian; Gattner, Michael; Weiss, Veronika; Brunner, Korbinian; Bretzler, Johanna; von Schirnding, Constantin; Torrano, Adriano A.; Spada, Fabio; Vrabel, Milan; Engelke, Hanna; Bräuchle, Christoph; Carell, Thomas; Bein, Thomas

    2016-04-01

    Effective and controlled drug delivery systems with on-demand release and targeting abilities have received enormous attention for biomedical applications. Here, we describe a novel enzyme-based cap system for mesoporous silica nanoparticles (MSNs) that is directly combined with a targeting ligand via bio-orthogonal click chemistry. The capping system is based on the pH-responsive binding of an aryl-sulfonamide-functionalized MSN and the enzyme carbonic anhydrase (CA). An unnatural amino acid (UAA) containing a norbornene moiety was genetically incorporated into CA. This UAA allowed for the site-specific bio-orthogonal attachment of even very sensitive targeting ligands such as folic acid and anandamide. This leads to specific receptor-mediated cell and stem cell uptake. We demonstrate the successful delivery and release of the chemotherapeutic agent Actinomycin D to KB cells. This novel nanocarrier concept provides a promising platform for the development of precisely controllable and highly modular theranostic systems.Effective and controlled drug delivery systems with on-demand release and targeting abilities have received enormous attention for biomedical applications. Here, we describe a novel enzyme-based cap system for mesoporous silica nanoparticles (MSNs) that is directly combined with a targeting ligand via bio-orthogonal click chemistry. The capping system is based on the pH-responsive binding of an aryl-sulfonamide-functionalized MSN and the enzyme carbonic anhydrase (CA). An unnatural amino acid (UAA) containing a norbornene moiety was genetically incorporated into CA. This UAA allowed for the site-specific bio-orthogonal attachment of even very sensitive targeting ligands such as folic acid and anandamide. This leads to specific receptor-mediated cell and stem cell uptake. We demonstrate the successful delivery and release of the chemotherapeutic agent Actinomycin D to KB cells. This novel nanocarrier concept provides a promising platform for the

  6. Dipolar recoupling NMR of biomolecular self-assemblies : determining inter- and intrastrand distances in fibrilized Alzheimer's {betta}-amyloid peptide.

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, D. M.; Senzinger, T. L. S.; Burkoth, T. S.; Miller-Auer, H.; Lynn, D. G.; Meredith, S. C.; Botto, R. E.; Chemistry; Univ. of Chicago

    1998-12-01

    data, taken together, refine the DRAWS method, and demonstrate its precision and utility in obtaining high resolution structural data in complex biomolecular aggregates such as A{beta}.

  7. Smartphones for cell and biomolecular detection.

    Science.gov (United States)

    Liu, Xiyuan; Lin, Tung-Yi; Lillehoj, Peter B

    2014-11-01

    Recent advances in biomedical science and technology have played a significant role in the development of new sensors and assays for cell and biomolecular detection. Generally, these efforts are aimed at reducing the complexity and costs associated with diagnostic testing so that it can be performed outside of a laboratory or hospital setting, requiring minimal equipment and user involvement. In particular, point-of-care (POC) testing offers immense potential for many important applications including medical diagnosis, environmental monitoring, food safety, and biosecurity. When coupled with smartphones, POC systems can offer portability, ease of use and enhanced functionality while maintaining performance. This review article focuses on recent advancements and developments in smartphone-based POC systems within the last 6 years with an emphasis on cell and biomolecular detection. These devices typically comprise multiple components, such as detectors, sample processors, disposable chips, batteries, and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. Researchers have demonstrated several promising approaches employing various detection schemes and device configurations, and it is expected that further developments in biosensors, battery technology and miniaturized electronics will enable smartphone-based POC technologies to become more mainstream tools in the scientific and biomedical communities.

  8. Transient response characteristics in a biomolecular integral controller.

    Science.gov (United States)

    Sen, Shaunak

    2016-04-01

    The cellular behaviour of perfect adaptation is achieved through the use of an integral control element in the underlying biomolecular circuit. It is generally unclear how integral action affects the important aspect of transient response in these biomolecular systems, especially in light of the fact that it typically deteriorates the transient response in engineering contexts. To address this issue, the authors investigated the transient response in a computational model of a simple biomolecular integral control system involved in bacterial signalling. They find that the transient response can actually speed up as the integral gain parameter increases. On further analysis, they find that the underlying dynamics are composed of slow and fast modes and the speed-up of the transient response is because of the speed-up of the slow-mode dynamics. Finally, they note how an increase in the integral gain parameter also leads to a decrease in the amplitude of the transient response, consistent with the overall improvement in the transient response. These results should be useful in understanding the overall effect of integral action on system dynamics, particularly for biomolecular systems.

  9. Exposing biomolecular properties one molecule at a time

    NARCIS (Netherlands)

    Elmalk, Abdalmohsen

    2012-01-01

    The work described in this thesis was aimed at the study of the functional properties of (isolated and purified) biomolecular systems at the single-molecule level. Two prerequisites are essential for successfully achieving this goal. First of all, single biomolecules should be observable, which mean

  10. Biomolecular recognition mechanisms studied by NMR spectroscopy and MD simulations

    NARCIS (Netherlands)

    Hsu, Shang-Te Danny

    2004-01-01

    This thesis describes the use of solution Nuclear Magnetic Resonance (NMR) spectroscopy and Molecular Dynamics (MD) simulations to study the mechanism of biomolecular recognition with two model systems: i) lipid II-binding lantibiotics (lanthionine-containing antibiotics) and ii) the human immunodef

  11. The biomolecular corona of nanoparticles in circulating biological media

    Science.gov (United States)

    Pozzi, D.; Caracciolo, G.; Digiacomo, L.; Colapicchioni, V.; Palchetti, S.; Capriotti, A. L.; Cavaliere, C.; Zenezini Chiozzi, R.; Puglisi, A.; Laganà, A.

    2015-08-01

    When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let multicomponent liposomes interact with fetal bovine serum (FBS) both statically and dynamically, i.e. in contact with circulating FBS (~40 cm s-1). The structure and composition of the liposome-protein corona, as determined by dynamic light scattering, electrophoretic light scattering and liquid chromatography tandem mass spectrometry, were found to be dependent on the incubation protocol. Specifically, following dynamic exposure to FBS, multicomponent liposomes were less enriched in complement proteins and appreciably more enriched in apolipoproteins and acute phase proteins (e.g. alpha-1-antitrypsin and inter-alpha-trypsin inhibitor heavy chain H3) that are involved in relevant interactions between nanoparticles and living systems. Supported by our results, we speculate that efficient predictive modeling of nanoparticle behavior in vivo will require accurate knowledge of nanoparticle-specific protein fingerprints in circulating biological media.When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let

  12. Radiation damage in biomolecular systems

    CERN Document Server

    Fuss, Martina Christina

    2012-01-01

    Since the discovery of X-rays and radioactivity, ionizing radiations have been widely applied in medicine both for diagnostic and therapeutic purposes. The risks associated with radiation exposure and handling led to the parallel development of the field of radiation protection. Pioneering experiments done by Sanche and co-workers in 2000 showed that low-energy secondary electrons, which are abundantly generated along radiation tracks, are primarily responsible for radiation damage through successive interactions with the molecular constituents of the medium. Apart from ionizing processes, which are usually related to radiation damage, below the ionization level low-energy electrons can induce molecular fragmentation via dissociative processes such as internal excitation and electron attachment. This prompted collaborative projects between different research groups from European countries together with other specialists from Canada,  the USA and Australia. This book summarizes the advances achieved by these...

  13. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

    OpenAIRE

    Wei, Guo Wei; Baker, Nathan A.

    2014-01-01

    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, el...

  14. Global Langevin model of multidimensional biomolecular dynamics

    Science.gov (United States)

    Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard

    2016-11-01

    Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F ( 𝒙 ) . To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F ( 𝒙 ) , which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

  15. Nonequilibrium phase transitions in biomolecular signal transduction

    Science.gov (United States)

    Smith, Eric; Krishnamurthy, Supriya; Fontana, Walter; Krakauer, David

    2011-11-01

    We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework.

  16. Combination of biomolecular and stable isotope techniques to determine the origin of organic matter used by bacterial communities: application to sediment

    NARCIS (Netherlands)

    Creach, V.; Lucas, F.; Deleu, C.; Bertru, G.; Mariotti, A.

    1999-01-01

    Natural isotopic composition is a good tool to trace organic matter in ecosystems. Recent studies used a combination of molecular and stable isotope techniques to determine the origin of the organic carbon used by bacteria in the water column. In our study, we show that this procedure can be used fo

  17. The fidelity of dynamic signaling by noisy biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Clive G Bowsher

    Full Text Available Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments.

  18. Physics at the biomolecular interface fundamentals for molecular targeted therapy

    CERN Document Server

    Fernández, Ariel

    2016-01-01

    This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood w...

  19. Stochastic Simulation of Biomolecular Networks in Dynamic Environments.

    Directory of Open Access Journals (Sweden)

    Margaritis Voliotis

    2016-06-01

    Full Text Available Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits.

  20. [Advances in biomolecular machine: methane monooxygenases].

    Science.gov (United States)

    Lu, Jixue; Wang, Shizhen; Fang, Baishan

    2015-07-01

    Methane monooxygenases (MMO), regarded as "an amazing biomolecular machine", catalyze the oxidation of methane to methanol under aerobic conditions. MMO catalyze the oxidation of methane elaborately, which is a novel way to catalyze methane to methanol. Furthermore, MMO can inspire the biomolecular machine design. In this review, we introduced MMO including structure, gene and catalytic mechanism. The history and the taxonomy of MMO were also introduced.

  1. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    B D Malhotra; Rahul Singhal

    2003-08-01

    Biomolecular electronics is rapidly evolving from physics, chemistry, biology, electronics and information technology. Organic materials such as proteins, pigments and conducting polymers have been considered as alternatives for carrying out the functions that are presently being performed by semiconductor silicon. Conducting polymers such as polypyrroles, polythiophenes and polyanilines have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices. Our group has been actively working towards the application of conducting polymers to Schottky diodes, metal–insulator–semiconductor (MIS) devices and biosensors for the past 10 years. This paper is a review of some of the results obtained at our laboratory in the area of conducting polymer biomolecular electronics.

  2. iBIOMES: managing and sharing biomolecular simulation data in a distributed environment.

    Science.gov (United States)

    Thibault, Julien C; Facelli, Julio C; Cheatham, Thomas E

    2013-03-25

    Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The system can be easily deployed on distributed servers to create a mini-grid at the researcher's site. The system not only offers a simple data deposition mechanism but also a way to register data into the system without moving the data from their original location. Any registered data set can be searched and downloaded using a set of defined metadata for molecular dynamics and quantum mechanics and visualized through a dynamic Web interface.

  3. RECENT PROGRESS IN BIOMOLECULAR NMR

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Structural genomics and proteomics were born from the understanding that functions of a protein are dictated by its 3D structure and dynamics. To understand protein functions on a genomic scale, we must know protein structures on a genomic scale. High resolution NMR can be used for this purpose. Traditional multidimensional NMR structure determination protocols become ineffective for structural genomics since to obtain a structure of a small protein of 15kD requires many months of painstaking spectral analysis and modeling. Recent advances in magnet and probe technology and in experimental methods have expanded the range of proteins amenable to structure determination and make the large scale structure determination possible. These advances are (1) effective expression systems for protein production, (2) introduction of cryoprobe, (3) structure determination with the use of the minimal amount of structural restraints obtained from the chemical shifts, residual dipolar couplings, NOEs, and computer modeling. In this talk,Iwill briefly outline these developments and related works done in our NMR lab.

  4. Origin of organic molecules and biomolecular homochirality.

    Science.gov (United States)

    Podlech, J

    2001-01-01

    Theories about the origin of biomolecular homochirality, which seems to be a prerequisite for the creation of life, are discussed. First, possible terrestrial and extraterrestrial sources of organic molecules are outlined. Then, mechanisms for the formation of enantiomerically enriched compounds and for the amplification of their chirality are described.

  5. Thermodynamic properties of water solvating biomolecular surfaces

    Science.gov (United States)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  6. Biomolecular Modification of Inorganic Crystal Growth

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J J

    2007-04-27

    The fascinating shapes and hierarchical designs of biomineralized structures are an inspiration to materials scientists because of the potential they suggest for biomolecular control over materials synthesis. Conversely, the failure to prevent or limit tissue mineralization in the vascular, skeletal, and urinary systems is a common source of disease. Understanding the mechanisms by which organisms direct or limit crystallization has long been a central challenge to the biomineralization community. One prevailing view is that mineral-associated macromolecules are responsible for either inhibiting crystallization or initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineralizing surfaces. In particular, biomolecules that present carboxyl groups to the growing crystal have been implicated as primary modulators of growth. Here we review the results from a combination of in situ atomic force microscopy (AFM) and molecular modeling (MM) studies to investigate the effect of specific interactions between carboxylate-rich biomolecules and atomic steps on crystal surfaces during the growth of carbonates, oxalates and phosphates of calcium. Specifically, we how the growth kinetics and morphology depend on the concentration of additives that include citrate, simple amino acids, synthetic Asp-rich polypeptides, and naturally occurring Asp-rich proteins found in both functional and pathological mineral tissues. The results reveal a consistent picture of shape modification in which stereochemical matching of modifiers to specific atomic steps drives shape modification. Inhibition and other changes in growth kinetics are shown to be due to a range of mechanisms that depend on chemistry and molecular size. Some effects are well described by classic crystal growth theories, but others, such as step acceleration due to peptide charge and hydrophylicity, were previously unrealized

  7. Bridging Nano- and Microtribology in Mechanical and Biomolecular Layers

    Science.gov (United States)

    Tomala, Agnieszka; Göçerler, Hakan; Gebeshuber, Ille C.

    The physical and chemical composition of surfaces determine various important properties of solids such as corrosion rates, adhesive properties, frictional properties, catalytic activity, wettability, contact potential and - finally and most importantly - failure mechanisms. Very thin, weak layers (of man-made and biological origin) on much harder substrates that reduce friction are the focus of the micro- and nanotribological investigations presented in this chapter.Biomolecular layers fulfil various functions in organs of the human body. Examples comprise the skin that provides a protective physical barrier between the body and the environment, preventing unwanted inward and outward passage of water and electrolytes, reducing penetration by destructive chemicals, arresting the penetration of microorganisms and external antigens and absorbing radiation from the sun, or the epithelium of the cornea that blocks the passage of foreign material, such as dust, water and bacteria, into the eye and that contributes to the lubrication layer that ensures smooth movement of the eyelids over the eyeballs.Monomolecular thin films, additive-derived reaction layers and hard coatings are widely used to tailor tribological properties of surfaces. Nanotribological investigations on these substrates can reveal novel properties regarding the orientation of chemisorbed additive layers, development of rubbing films with time and the relation of frictional properties to surface characteristics in diamond coatings.Depending on the questions to be answered with the tribological research, various micro- and nanotribological measurement methods are applied, including scanning probe microscopy (AFM, FFM), scanning electron microscopy, microtribometer investigations, angle-resolved photoelectron spectroscopy and optical microscopy. Thoughts on the feasibility of a unified approach to energy-dissipating systems and how it might be reached (touching upon new ways of scientific publishing

  8. Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study.

    Science.gov (United States)

    Hu, Xiaohua; Ng, Michael; Wu, Fang-Xiang; Sokhansanj, Bahrad A

    2009-03-01

    In this paper, we present a novel method to mine, model, and evaluate a regulatory system executing cellular functions that can be represented as a biomolecular network. Our method consists of two steps. First, a novel scale-free network clustering approach is applied to such a biomolecular network to obtain various subnetworks. Second, computational models are generated for the subnetworks and simulated to predict their behavior in the cellular context. We discuss and evaluate some of the advanced computational modeling approaches, in particular, state-space modeling, probabilistic Boolean network modeling, and fuzzy logic modeling. The modeling and simulation results represent hypotheses that are tested against high-throughput biological datasets (microarrays and/or genetic screens) under normal and perturbation conditions. Experimental results on time-series gene expression data for the human cell cycle indicate that our approach is promising for subnetwork mining and simulation from large biomolecular networks.

  9. Global analysis of time-resolved fluorescence microspectroscopy and applications in biomolecular studies

    NARCIS (Netherlands)

    Laptenok, S.

    2009-01-01

    Understanding the properties of biomolecular networks is of central importance in life sciences. Optical microscopy has been very useful to determine the sub-cellular localisation of proteins but it cannot reveal whether proteins interact with one another. Micro-spectroscopic techniques (combining m

  10. 核磁共振、X射线小角散射以及计算机模拟相结合构建生物大分子复合物的结构模型%Determining Structural Models of Biomolecular Complexes Integrating Nuclear Magnetic Resonance, Small-Angle X-ray Scattering and Computational Simulations

    Institute of Scientific and Technical Information of China (English)

    彭俊辉; 赵德彪; 文彬; 张志勇

    2015-01-01

    Structural biology has been paying more attention on biomolecular complexes over the past decades, since they are crucial for many biological processes. Among these techniques for structural determination, nuclear magnetic resonance (NMR) has its advantage when dealing with biomolecules with high flexibility in solution. Small-angle X-ray scattering (SAXS) is a very important complementary technique that provides information on global shape of biomolecules. For biomolecular complexes, it can be much easier to determine atomic structures of individual subunits through NMR. In addition, NMR can also provide other structural information, such as the interface and orientations between subunits, and long range distance and angular restraints. Therefore, to construct structural models of biomolecular complexes, it would be very appropriate to combine experimental restraints obtained through NMR and low-resolution shape information from SAXS by utilizing computational tools, which is the main topic of this review.%近年来,结构生物学研究越来越注重生物大分子复合物的解析,因为许多重要生物学过程都离不开复合物的参与.溶液核磁共振是目前重要的结构解析方法之一.X射线小角散射(SAXS)作为一种新的结构生物学实验手段,近年来发展迅速.SAXS 能提供生物大分子复合物的较低分辨率结构信息,而核磁共振能解析复合物中各个亚基的原子分辨率结构.此外,通过核磁共振还能得到亚基之间的界面、取向以及距离信息.因此近年来通过计算机模拟,整合核磁共振和 SAXS 不同分辨率的结构信息,可以用来搭建生物大分子复合物的结构模型.该综述重点介绍这方面的研究进展.

  11. System for determining biofuel concentration

    Energy Technology Data Exchange (ETDEWEB)

    Huff, Shean P.; Janke, Christopher James; Kass, Michael D.; Lewis, Sr, Samuel Arthur; Pawel, Steven J; Theiss, Timothy J.

    2016-09-13

    A measurement device or system configured to measure the content of biofuels within a fuel blend. By measuring a state of a responsive material within a fuel blend, a biofuel content of the fuel blend may be measured. For example, the solubility of a responsive material to biofuel content within a fuel blend, may affect a property of the responsive material, such as shape, dimensional size, or electrical impedance, which may be measured and used as a basis for determining biofuel content.

  12. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  13. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  14. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ping Cheng

    2010-03-01

    Full Text Available The combination of nanodiamond (ND with biomolecular mass spectrometry (MS makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase extraction and elution on NDs and different application examples including peptide, protein, DNA, glycan and others. Owing to the quick development of nanotechnology, surface chemistry, new MS methods and the intense interest in proteomics and genomics, a huge increase of their applications in biomolecular MS analysis in the near future can be predicted.

  15. A statistical mechanical description of biomolecular hydration

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-02-01

    We present an efficient and accurate theoretical description of the structural hydration of biological macromolecules. The hydration of molecules of almost arbitrary size (tRNA, antibody-antigen complexes, photosynthetic reaction centre) can be studied in solution and in the crystal environment. The biomolecular structure obtained from x-ray crystallography, NMR, or modeling is required as input information. The structural arrangement of water molecules near a biomolecular surface is represented by the local water density analogous to the corresponding electron density in an x-ray diffraction experiment. The water-density distribution is approximated in terms of two- and three-particle correlation functions of solute atoms with water using a potentials-of-mean-force expansion.

  16. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    OpenAIRE

    Ping Cheng; Xianglei Kong

    2010-01-01

    The combination of nanodiamond (ND) with biomolecular mass spectrometry (MS) makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase...

  17. Biomolecular decision-making process for self assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Osbourn, Gordon Cecil

    2005-01-01

    The brain is often identified with decision-making processes in the biological world. In fact, single cells, single macromolecules (proteins) and populations of molecules also make simple decisions. These decision processes are essential to survival and to the biological self-assembly and self-repair processes that we seek to emulate. How do these tiny systems make effective decisions? How do they make decisions in concert with a cooperative network of other molecules or cells? How can we emulate the decision-making behaviors of small-scale biological systems to program and self-assemble microsystems? This LDRD supported research to answer these questions. Our work included modeling and simulation of protein populations to help us understand, mimic, and categorize molecular decision-making mechanisms that nonequilibrium systems can exhibit. This work is an early step towards mimicking such nanoscale and microscale biomolecular decision-making processes in inorganic systems.

  18. Quartz crystal microbalance: a useful tool for studying thin polymer films and complex biomolecular systems at the solution-surface interface.

    Science.gov (United States)

    Marx, Kenneth A

    2003-01-01

    The quartz crystal microbalance (QCM) is a simple, cost effective, high-resolution mass sensing technique, based upon the piezoelectric effect. As a methodology, the QCM evolved a solution measurement capability in largely analytical chemistry and electrochemistry applications due to its sensitive solution-surface interface measurement capability. The technique possesses a wide detection range. At the low mass end, it can detect monolayer surface coverage by small molecules or polymer films. At the upper end, it is capable of detecting much larger masses bound to the surface. These can be complex arrays of biopolymers and biomacromolecules, even whole cells. In addition, the QCM can provide information about the energy dissipating properties of the bound surface mass. Another important and unique feature of the technique is the ability to measure mass and energy dissipation properties of films while simultaneously carrying out electrochemistry on solution species or upon film systems bound to the upper electrode on the oscillating quartz crystal surface. These measurements can describe the course of electropolymerization of a film or can reveal ion or solute transport within a film during changes in the film environment or state, including the oxidation state for an electroactive film driven by the underlying surface potential. The past decade has witnessed an explosive growth in the application of the QCM technique to the study of a wide range of molecular systems at the solution-surface interface, in particular, biopolymer and biochemical systems. In this report, we start with a brief historical and technical overview. Then we discuss the application of the QCM technique to measurements involving micellar systems, self-assembling monolayers and their phase transition behavior, molecularly imprinted polymers, chemical sensors, films formed using the layer-by-layer assembly technique, and biopolymer films and point out the utility of the electrochemical

  19. Computational and theoretical aspects of biomolecular structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Berendzen, J.; Catasti, P., Chen, X. [and others

    1996-09-01

    This is the final report for a project that sought to evaluate and develop theoretical, and computational bases for designing, performing, and analyzing experimental studies in structural biology. Simulations of large biomolecular systems in solution, hydrophobic interactions, and quantum chemical calculations for large systems have been performed. We have developed a code that implements the Fast Multipole Algorithm (FMA) that scales linearly in the number of particles simulated in a large system. New methods have been developed for the analysis of multidimensional NMR data in order to obtain high resolution atomic structures. These methods have been applied to the study of DNA sequences in the human centromere, sequences linked to genetic diseases, and the dynamics and structure of myoglobin.

  20. Design and implementation of a biomolecular concentration tracker.

    Science.gov (United States)

    Hsiao, Victoria; de los Santos, Emmanuel L C; Whitaker, Weston R; Dueber, John E; Murray, Richard M

    2015-02-20

    As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in Escherichia coli and that steady state outputs can be tuned.

  1. Biomolecular interactions: essential instrumentation methods.

    Science.gov (United States)

    Messina, Paula Veronica; Ruso, Juan Manuel

    2013-01-01

    The main goal of this review is to outline the basic principles and applications of the broad range of modern biophysical technical methods used to study the different aspects of protein–ligand interactions by discussing such aspects as newer systems, unusual approaches and highly used techniques.

  2. Barcoded microchips for biomolecular assays.

    Science.gov (United States)

    Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu

    2015-01-20

    Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

  3. Azurin for Biomolecular Electronics: a Reliability Study

    Science.gov (United States)

    Bramanti, Alessandro; Pompa, Pier Paolo; Maruccio, Giuseppe; Calabi, Franco; Arima, Valentina; Cingolani, Roberto; Corni, Stefano; Di Felice, Rosa; De Rienzo, Francesca; Rinaldi, Ross

    2005-09-01

    The metalloprotein azurin, used in biomolecular electronics, is investigated with respect to its resilience to high electric fields and ambient conditions, which are crucial reliability issues. Concerning the effect of electric fields, two models of different complexity agree indicating an unexpectedly high robustness. Experiments in device-like conditions confirm that no structural modifications occur, according to fluorescence spectra, even after a 40-min exposure to tens of MV/m. Ageing is then investigated experimentally, at ambient conditions and without field, over several days. Only a small conformational rearrangement is observed in the first tens of hours, followed by an equilibrium state.

  4. Nanotube-Based Chemical and Biomolecular Sensors

    Institute of Scientific and Technical Information of China (English)

    J.Koh; B.Kim; S.Hong; H.Lim; H.C.Choi

    2008-01-01

    We present a brief review about recent results regarding carbon nanotube (CNT)-based chemical and biomolecular sensors. For the fabrication of CNT-based sensors, devices containing CNT channels between two metal electrodes are first fabricated usually via chemical vapor deposition (CVD) process or "surface programmed assembly" method. Then, the CNT surfaces are often functionalized to enhance the selectivity of the sensors. Using this process, highly-sensitive CNT-based sensors can be fabricated for the selective detection of various chemical and biological molecules such as hydrogen, ammonia, carbon monoxide, chlorine gas, DNA, glucose, alcohol, and proteins.

  5. Fundamentos biomoleculares de la diabetes mellitus

    OpenAIRE

    2013-01-01

    La diabetes mellitus es una enfermedad endocrina con importantes implicaciones a nivel sistémico, como: angiopatía, neuropatía, retinopatía y nefropatía, entre otras. Estas  complicaciones tienen su origen en eventos biomoleculares desencadenados por la hiperglicemia.  La presente revisión de tema trata sobre la estructura y síntesis de la insulina en las células β del páncreas; los eventos moleculares y bioquímicos que activan su secreción como respuesta a una alta concentración de glucosa e...

  6. Systematic evaluation of bundled SPC water for biomolecular simulations.

    Science.gov (United States)

    Gopal, Srinivasa M; Kuhn, Alexander B; Schäfer, Lars V

    2015-04-07

    In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. In the present work, we systematically validated and critically tested bundled SPC water models as solvent for biomolecular simulations. To that aim, we investigated both thermodynamic and structural properties of various biomolecular systems through molecular dynamics (MD) simulations. Potentials of mean force of dimerization of pairs of amino acid side chains as well as hydration free energies of single side chains obtained with bundled SPC and standard (unrestrained) SPC water agree closely with each other and with experimental data. Decomposition of the hydration free energies into enthalpic and entropic contributions reveals that in bundled SPC, this favorable agreement of the free energies is due to a larger degree of error compensation between hydration enthalpy and entropy. The Ramachandran maps of Ala3, Ala5, and Ala7 peptides are similar in bundled and unrestrained SPC, whereas for the (GS)2 peptide, bundled water leads to a slight overpopulation of extended conformations. Analysis of the end-to-end distance autocorrelation times of the Ala5 and (GS)2 peptides shows that sampling in more viscous bundled SPC water is about two times slower. Pronounced differences between the water models were found for the structure of a coiled-coil dimer, which is instable in bundled SPC but not in standard SPC. In addition, the hydration of the active site of the serine protease α-chymotrypsin depends on the water model. Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water

  7. Biomolecular Network-Based Synergistic Drug Combination Discovery

    Directory of Open Access Journals (Sweden)

    Xiangyi Li

    2016-01-01

    Full Text Available Drug combination is a powerful and promising approach for complex disease therapy such as cancer and cardiovascular disease. However, the number of synergistic drug combinations approved by the Food and Drug Administration is very small. To bridge the gap between urgent need and low yield, researchers have constructed various models to identify synergistic drug combinations. Among these models, biomolecular network-based model is outstanding because of its ability to reflect and illustrate the relationships among drugs, disease-related genes, therapeutic targets, and disease-specific signaling pathways as a system. In this review, we analyzed and classified models for synergistic drug combination prediction in recent decade according to their respective algorithms. Besides, we collected useful resources including databases and analysis tools for synergistic drug combination prediction. It should provide a quick resource for computational biologists who work with network medicine or synergistic drug combination designing.

  8. Stochastic Simulation of Biomolecular Reaction Networks Using the Biomolecular Network Simulator Software

    Science.gov (United States)

    2008-02-01

    investigate the simulation of a biomolecular reaction network with BNS, a simple model of a generic self-assembling catalytic ligation reaction in a...Amino Acid Pools Nucleotide Triphosphate Pools Nucleotide Monophosphate Pools Ligation Reaction 1551 517 7 RESULTS Simulation of exemplar...and reaction r8 is the catalytic ligation reaction . In figures 5(B) through 5(F), both the time-averaged event rate for a single simulation run

  9. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari

    2009-01-01

    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  10. Biomolecular rods and tubes in nanotechnology

    Science.gov (United States)

    Bittner, Alexander M.

    2005-02-01

    Biomolecules are vitally important elements in nanoscale science and also in future nanotechnology. Their shape and their chemical and physical functionality can give them a big advantage over inorganic and organic substances. While this becomes most obvious in proteins and peptides, with their complicated, but easily controlled chemistry, other biomolecular substances such as DNA, lipids and carbohydrates can also be important. In this review, the emphasis is on one-dimensional molecules and on molecules that self-assemble into linear structures, and on their potential applications. An important aspect is that biomolecules can act as templates, i.e. their shape and chemical properties can be employed to arrange inorganic substances such as metals or metal compounds on the nanometre scale. In particular, rod- and tube-like nanostructures can show physical properties that are different from those of the bulk material, and thus these structures are likely to be a basis for new technology.

  11. Fundamentos biomoleculares de la diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Katiana Mendoza

    2013-12-01

    Full Text Available La diabetes mellitus es una enfermedad endocrina con importantes implicaciones a nivel sistémico, como: angiopatía, neuropatía, retinopatía y nefropatía, entre otras. Estas  complicaciones tienen su origen en eventos biomoleculares desencadenados por la hiperglicemia.  La presente revisión de tema trata sobre la estructura y síntesis de la insulina en las células β del páncreas; los eventos moleculares y bioquímicos que activan su secreción como respuesta a una alta concentración de glucosa en sangre; la cascada de señalización generada por la unión de la insulina a su receptor sobre células diana; y las alteraciones metabólicas que los diferentes tipos de diabetes mellitus producen.

  12. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic.

    Science.gov (United States)

    Privman, Vladimir; Halámek, Jan; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-11-11

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H(2)O(2) was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

  13. Out-of-equilibrium biomolecular interactions monitored by picosecond fluorescence in microfluidic droplets.

    Science.gov (United States)

    Maillot, Sacha; Carvalho, Alain; Vola, Jean-Pierre; Boudier, Christian; Mély, Yves; Haacke, Stefan; Léonard, Jérémie

    2014-05-21

    We developed a new experimental approach combining Time-Resolved Fluorescence (TRF) spectroscopy and Droplet Microfluidics (DμF) to investigate the relaxation dynamics of structurally heterogeneous biomolecular systems. Here DμF was used to produce with minimal material consumption an out-of-equilibrium, fluorescently labeled biomolecular complex by rapid mixing within the droplets. TRF detection was implemented with a streak camera to monitor the time evolution of the structural heterogeneity of the complex along its relaxation towards equilibrium while it propagates inside the microfluidic channel. The approach was validated by investigating the fluorescence decay kinetics of a model interacting system of bovine serum albumin and Patent Blue V. Fluorescence decay kinetics are acquired with very good signal-to-noise ratio and allow for global, multicomponent fluorescence decay analysis, evidencing heterogeneous structural relaxation over several 100 ms.

  14. Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy.

    Science.gov (United States)

    Yang, Yong; Wang, Hong; Erie, Dorothy A

    2003-02-01

    Atomic force microscopy (AFM) has been applied in many biological investigations in the past 15 years. This review focuses on the application of AFM for quantitatively characterizing the structural and thermodynamic properties of protein-protein and protein-nucleic acid complexes. AFM can be used to determine the stoichiometries and association constants of multiprotein assemblies and to quantify changes in conformations of proteins and protein-nucleic acid complexes. In addition, AFM in solution permits the observation of the dynamic properties of biomolecular complexes and the measurement of intermolecular forces between biomolecules. Recent advances in cryogenic AFM, AFM on two-dimensional crystals, carbon nanotube probes, solution imaging, high-speed AFM, and manipulation capabilities enhance these applications by improving AFM resolution and the dynamic and operative capabilities of the AFM. These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation.

  15. Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches.

    Science.gov (United States)

    Gutiérrez, R; Caetano, R A; Woiczikowski, B P; Kubar, T; Elstner, M; Cuniberti, G

    2009-05-22

    We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

  16. A starting point for fluorescence-based single-molecule measurements in biomolecular research.

    Science.gov (United States)

    Gust, Alexander; Zander, Adrian; Gietl, Andreas; Holzmeister, Phil; Schulz, Sarah; Lalkens, Birka; Tinnefeld, Philip; Grohmann, Dina

    2014-09-30

    Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  17. A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation.

    Science.gov (United States)

    Wu, Songlin; Wang, Pei; Xiao, Chen; Li, Zheng; Yang, Bing; Fu, Jieyang; Chen, Jing; Wan, Neng; Ma, Cong; Li, Maoteng; Yang, Xiangliang; Zhan, Yi

    2016-08-10

    Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.

  18. A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research

    Directory of Open Access Journals (Sweden)

    Alexander Gust

    2014-09-01

    Full Text Available Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  19. PREFACE: India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation

    Science.gov (United States)

    Onoda, Mitsuyoshi; Malhotra, Bansi D.

    2012-04-01

    The 'India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation' (IJWBME 2011) will be held on 7-10 December 2011 at EGRET Himeji, Himeji, Hyogo, Japan. This workshop was held for the first time on 17-19 December 2009 at NPL, New Delhi. Keeping in mind the importance of organic nanotechnology and biomolecular electronics for environmental preservation and their anticipated impact on the economics of both the developing and the developed world, IJWBME 2009 was jointly organized by the Department of Biological Functions, Graduate School of Life Sciences and Systems Engineering, the Kyushu Institute of Technology (KIT), Kitakyushu, Japan, and the Department of Science & Technology Centre on Biomolecular Electronics (DSTCBE), National Physical Laboratory (NPL). Much progress in the field of biomolecular electronics and organic nanotechnology for environmental preservation is expected for the 21st Century. Organic optoelectronic devices, such as organic electroluminescent devices, organic thin-film transistors, organic sensors, biological systems and so on have especially attracted much attention. The main purpose of this workshop is to provide an opportunity for researchers interested in biomolecular electronics and organic nanotechnology for environmental preservation, to come together in an informal and friendly atmosphere and exchange technical knowledge and experience. We are sure that this workshop will be very useful and fruitful for all participants in summarizing the recent progress in biomolecular electronics and organic nanotechnology for environmental preservation and preparing new ground for the next generation. Many papers have been submitted from India and Japan and more than 30 papers have been accepted for presentation. The main topics of interest are as follows: Bioelectronics Biomolecular Electronics Fabrication Techniques Self-assembled Monolayers Nano-sensors Environmental Monitoring Organic Devices

  20. Attitude Determination and Control Systems

    Science.gov (United States)

    Starin, Scott R.; Eterno, John

    2011-01-01

    designing and operating spacecraft pointing (i.e. attitude) systems.

  1. Electrochemical sensor for multiplex screening of genetically modified DNA: identification of biotech crops by logic-based biomolecular analysis.

    Science.gov (United States)

    Liao, Wei-Ching; Chuang, Min-Chieh; Ho, Ja-An Annie

    2013-12-15

    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO.

  2. Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions.

    Science.gov (United States)

    Carter, Megan; Voth, Andrea Regier; Scholfield, Matthew R; Rummel, Brittany; Sowers, Lawrence C; Ho, P Shing

    2013-07-23

    Interest in noncovalent interactions involving halogens, particularly halogen bonds (X-bonds), has grown dramatically in the past decade, propelled by the use of X-bonding in molecular engineering and drug design. However, it is clear that a complete analysis of the structure-energy relationship must be established in biological systems to fully exploit X-bonds for biomolecular engineering. We present here the first comprehensive experimental study to correlate geometries with their stabilizing potentials for fluorine (F), chlorine (Cl), bromine (Br), or iodine (I) X-bonds in a biological context. For these studies, we determine the single-crystal structures of DNA Holliday junctions containing halogenated uracil bases that compete X-bonds against classic hydrogen bonds (H-bonds), estimate the enthalpic energies of the competing interactions in the crystal system through crystallographic titrations, and compare the enthalpic and entropic energies of bromine and iodine X-bonds in solution by differential scanning calorimetry. The culmination of these studies demonstrates that enthalpic stabilization of X-bonds increases with increasing polarizability from F to Cl to Br to I, which is consistent with the σ-hole theory of X-bonding. Furthermore, an increase in the X-bonding potential is seen to direct the interaction toward a more ideal geometry. However, the entropic contributions to the total free energies must also be considered to determine how each halogen potentially contributes to the overall stability of the interaction. We find that bromine has the optimal balance between enthalpic and entropic energy components, resulting in the lowest free energy for X-bonding in this DNA system. The X-bond formed by iodine is more enthalpically stable, but this comes with an entropic cost, which we attribute to crowding effects. Thus, the overall free energy of an X-bonding interaction balances the stabilizing electrostatic effects of the σ-hole against the competing

  3. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    Directory of Open Access Journals (Sweden)

    Nielsen Jens

    2008-02-01

    Full Text Available Abstract Background Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results Here we introduce a hypothesis-driven method that integrates bio-molecular network topology with transcriptome data, thereby allowing the identification of key biological features (Reporter Features around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription Factors, Reporter Proteins and Reporter Complexes, and use this to decipher the logic of regulatory circuits playing a key role in yeast glucose repression and human diabetes. Conclusion Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks that are significantly affected between or across conditions. Results of the Reporter Feature analysis not only provide a snapshot of the transcriptional regulatory program but also are biologically easy to interpret and provide a powerful way to generate new hypotheses. Our Reporter Features analyses of yeast glucose repression and human diabetes data brings hints towards the understanding of the principles of transcriptional regulation controlling these two important and potentially closely related systems.

  4. A fast mollified impulse method for biomolecular atomistic simulations

    Science.gov (United States)

    Fath, L.; Hochbruck, M.; Singh, C. V.

    2017-03-01

    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice-ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  5. Identification of determinism in noisy neuronal systems.

    Science.gov (United States)

    Slutzky, Marc W; Cvitanovic, Predrag; Mogul, David J

    2002-08-30

    Most neuronal ensembles are nonlinear excitable systems. Thus it is becoming common to apply principles derived from nonlinear dynamics to characterize neuronal systems. One important characterization is whether such systems contain deterministic behavior or are purely stochastic. Unfortunately, many methods used to make this distinction do not perform well when both determinism and high-amplitude noise are present which is often the case in physiological systems. Therefore, we propose two novel techniques for identifying determinism in experimental systems. The first, called short-time expansion analysis, examines the expansion rate of small groups of points in state space. The second, called state point forcing, derives from the technique of chaos control. The system state is forced onto a fixed point, and the subsequent behavior is analyzed. This technique can be used to verify the presence of fixed points (or unstable periodic orbits) and to assess stationarity. If these are present, it implies that the system contains determinism. We demonstrate the use and possible limitations of these two techniques in two systems: the Hénon map, a classic example of a chaotic system, and spontaneous epileptiform bursting in the rat hippocampal slice. Identifying the presence of determinism in a physiological system assists in the understanding of the system's dynamics and provides a mechanism for manipulating this behavior.

  6. Label-free screening of bio-molecular interactions.

    Science.gov (United States)

    Cooper, Matthew A

    2003-11-01

    The majority of techniques currently employed to interrogate a biomolecular interaction require some type of radio- or enzymatic- or fluorescent-labelling to report the binding event. However, there is an increasing awareness of novel techniques that do not require labelling of the ligand or the receptor, and that allow virtually any complex to be screened with minimal assay development. This review focuses on three major label-free screening platforms: surface plasmon resonance biosensors, acoustic biosensors, and calorimetric biosensors. Scientists in both academia and industry are using biosensors in areas that encompass almost all areas drug discovery, diagnostics, and the life sciences. The capabilities and advantages of each technique are compared and key applications involving small molecules, proteins, oligonucleotides, bacteriophage, viruses, bacteria, and cells are reviewed. The role of the interface between the biosensor surface (in the case of SPR and acoustic biosensors) and the chemical or biological systems to be studied is also covered with attention to the covalent and non-covalent coupling chemistries commonly employed.

  7. A mechanical Turing machine: blueprint for a biomolecular computer.

    Science.gov (United States)

    Shapiro, Ehud

    2012-08-06

    We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may 'compute' synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications.

  8. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.; van Dijk, M.; Bonvin, A.M.J.J.

    2010-01-01

    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  9. Biomolecular interactions in HCV nucleocapsid-like particles as revealed by vibrational spectroscopy

    Science.gov (United States)

    Rodríguez-Casado, Arantxa; Molina, Marina; Carmona, Pedro

    2007-05-01

    Hepatitis C virus (HCV) occurs in the form of 55-65 nm spherical particles, but the structure of the virion remains to be clarified. Structural studies of HCV have been hampered by the lack of an appropriate cell culture system. However, structural analyses of HCV components can provide an essential framework for understanding of the molecular mechanism of virion assembly. This article reviews the potential of vibrational spectroscopy aimed at the knowledge of HCV structural biology, particularly regarding biomolecular interactions in nucleocapsid-like particles obtained in vitro.

  10. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-10-01

    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  11. Lunar Navigation Determination System - LaNDS

    Science.gov (United States)

    Quinn, David; Talabac, Stephen

    2012-01-01

    A portable comprehensive navigational system has been developed that both robotic and human explorers can use to determine their location, attitude, and heading anywhere on the lunar surface independent of external infrastructure (needs no Lunar satellite network, line of sight to the Sun or Earth, etc.). The system combines robust processing power with an extensive topographical database to create a real-time atlas (GIS Geospatial Information System) that is able to autonomously control and monitor both single unmanned rovers and fleets of rovers, as well as science payload stations. The system includes provisions for teleoperation and tele-presence. The system accepts (but does not require) inputs from a wide range of sensors. A means was needed to establish a location when the search is taken deep in a crater (looking for water ice) and out of view of Earth or any other references. A star camera can be employed to determine the user's attitude in menial space and stellar map in body space. A local nadir reference (e.g., an accelerometer that orients the nadir vector in body space) can be used in conjunction with a digital ephemeris and gravity model of the Moon to isolate the latitude, longitude, and azimuth of the user on the surface. That information can be used in conjunction with a Lunar GIS and advanced navigation planning algorithms to aid astronauts (or other assets) to navigate on the Lunar surface.

  12. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

    Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  13. Polygenic sex determination system in zebrafish.

    Directory of Open Access Journals (Sweden)

    Woei Chang Liew

    Full Text Available BACKGROUND: Despite the popularity of zebrafish as a research model, its sex determination (SD mechanism is still unknown. Most cytogenetic studies failed to find dimorphic sex chromosomes and no primary sex determining switch has been identified even though the assembly of zebrafish genome sequence is near to completion and a high resolution genetic map is available. Recent publications suggest that environmental factors within the natural range have minimal impact on sex ratios of zebrafish populations. The primary aim of this study is to find out more about how sex is determined in zebrafish. METHODOLOGY/PRINCIPAL FINDINGS: Using classical breeding experiments, we found that sex ratios across families were wide ranging (4.8% to 97.3% males. On the other hand, repeated single pair crossings produced broods of very similar sex ratios, indicating that parental genotypes have a role in the sex ratio of the offspring. Variation among family sex ratios was reduced after selection for breeding pairs with predominantly male or female offspring, another indication that zebrafish sex is regulated genetically. Further examinations by a PCR-based "blind assay" and array comparative genomic hybridization both failed to find universal sex-linked differences between the male and female genomes. Together with the ability to increase the sex bias of lines by selective breeding, these data suggest that zebrafish is unlikely to utilize a chromosomal sex determination (CSD system. CONCLUSIONS/SIGNIFICANCE: Taken together, our study suggests that zebrafish sex is genetically determined with limited, secondary influences from the environment. As we have not found any sign for CSD in the species, we propose that the zebrafish has a polygenic sex determination system.

  14. Determination of stakeholders' consensus over values of system of systems

    NARCIS (Netherlands)

    Rajabalinejad, Mohammad; Bonnema, G. Maarten

    2014-01-01

    This paper focuses on one of the earliest steps in System of Systems (SoS) design aiming to meaningfully determine stakeholders’ values or preferences. It recommends the plural problem definition and dynamic construction of stakeholder’s values in the front end of design process. It suggests a metho

  15. Fuzzy logic in indoor position determination system

    Directory of Open Access Journals (Sweden)

    Michał Socha

    2016-12-01

    Full Text Available The article outlines how to use the convergence of collections to determine the position of a mobile device based on the WiFi radio signal strength with the use of fuzzy sets. The main aim is the development of the method for indoor position determination based on existing WiFi network infrastructure indoors. The approach is based on the WiFi radio infrastructure existing inside the buildings and requires operating mobile devices such as smartphones or tablets. An SQL database engine is also necessary as a widespread data interface. The SQL approach is not limited to the determination of the position but also to the creation of maps in which the system defining the position of the mobile device will operate. In addition, implementation issues are presented along with the distribution of the burden of performing calculations and the benefits of such an approach for determining the location. The authors describe how to decompose the task of determining the position in a client-server architecture.

  16. Systems and Methods for Determining Inertial Navigation System Faults

    Science.gov (United States)

    Bharadwaj, Raj Mohan (Inventor); Bageshwar, Vibhor L. (Inventor); Kim, Kyusung (Inventor)

    2017-01-01

    An inertial navigation system (INS) includes a primary inertial navigation system (INS) unit configured to receive accelerometer measurements from an accelerometer and angular velocity measurements from a gyroscope. The primary INS unit is further configured to receive global navigation satellite system (GNSS) signals from a GNSS sensor and to determine a first set of kinematic state vectors based on the accelerometer measurements, the angular velocity measurements, and the GNSS signals. The INS further includes a secondary INS unit configured to receive the accelerometer measurements and the angular velocity measurements and to determine a second set of kinematic state vectors of the vehicle based on the accelerometer measurements and the angular velocity measurements. A health management system is configured to compare the first set of kinematic state vectors and the second set of kinematic state vectors to determine faults associated with the accelerometer or the gyroscope based on the comparison.

  17. Application of Frontal Affinity Chromatography to Study the Biomolecular Interactions with Trypsin.

    Science.gov (United States)

    Hu, YuanYuan; Qian, Junqing; Guo, Hui; Jiang, ShengLan; Zhang, Zheng

    2015-07-01

    Trypsin is a serine protease that has been proposed as a potential therapeutic target for metabolic disorders and malignancy diseases, thus the identification of biomolecular interactions of compounds to trypsin could be of great therapeutic importance. In this study, trypsin was immobilized on a monolithic silica capillary column via sol-gel. The binding properties of four small molecules (daidzin, genistin, matrine and oxymatrine) to trypsin were examined using the trypsin affinity columns by frontal analysis. The results indicate that the matrine (dissociation constant, Kd = 7.904 μM) has stronger interaction with trypsin than the oxymatrine (Kd = 8.204 μM), whereas daidzin and genistin were nearly have no affinity with trypsin. The results demonstrated that the frontal affinity chromatography can be used for the direct determination of protein-protease inhibitor binding interactions and have several significant advantages, including easy fabricating, reproducible, minimal technological requirements and potential to become a reliable alternative for quantitative studies of biomolecular interactions.

  18. Biomolecular recognition and detection using gold-based nanoprobes

    Science.gov (United States)

    Crew, Elizabeth

    The ability to control the biomolecular interactions is important for developing bioanalytical probes used in biomolecule and biomarker detections. This work aims at a fundamental understanding of the interactions and reactivities involving DNA, miRNA, and amino acids using gold-based nanoparticles as nanoprobes, which has implications for developing new strategies for the early detection of diseases, such as cancer, and controlled delivery of drugs. Surface modifications of the nanoprobes with DNA, miRNA, and amino acids and the nanoprobe directed biomolecular reactivities, such as complementary-strand binding, enzymatic cutting and amino acid interactions, have been investigated. Among various analytical techniques employed for the analysis of the biomolecule-nanoprobe interactions, surface enhanced Raman scattering spectroscopy (SERS) has been demonstrated to provide a powerful tool for real time monitoring of the DNA assembly and enzymatic cutting processes in solutions. This demonstration harnesses the "hot-spot" characteristic tuned by the interparticle biomolecular-regulated interactions and distances. The assembly of gold nanoparticles has also been exploited as sensing thin films on chemiresistor arrays for the detection of volatile organic compounds, including biomarker molecules associated with diabetes. Important findings of the nanoprobes in delivering miRNA to cells, detecting DNA hybridization kinetics, discerning chiral recognition with enantiomeric cysteines, and sensing biomarker molecules with the nanostructured thin films will be discussed, along with their implications to enhancing sensitivity, selectivity and limits of detection.

  19. Solution influence on biomolecular equilibria - Nucleic acid base associations

    Science.gov (United States)

    Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

    1984-01-01

    Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

  20. Photochemical functionalization of gallium nitride thin films with molecular and biomolecular layers.

    Science.gov (United States)

    Kim, Heesuk; Colavita, Paula E; Metz, Kevin M; Nichols, Beth M; Sun, Bin; Uhlrich, John; Wang, Xiaoyu; Kuech, Thomas F; Hamers, Robert J

    2006-09-12

    We demonstrate that photochemical functionalization can be used to functionalize and photopattern the surface of gallium nitride crystalline thin films with well-defined molecular and biomolecular layers. GaN(0001) surfaces exposed to a hydrogen plasma will react with organic molecules bearing an alkene (C=C) group when illuminated with 254 nm light. Using a bifunctional molecule with an alkene group at one end and a protected amine group at the other, this process can be used to link the alkene group to the surface, leaving the protected amine exposed. Using a simple contact mask, we demonstrate the ability to directly pattern the spatial distribution of these protected amine groups on the surface with a lateral resolution of <12 mum. After deprotection of the amines, single-stranded DNA oligonucleotides were linked to the surface using a bifunctional cross-linker. Measurements using fluorescently labeled complementary and noncomplementary sequences show that the DNA-modified GaN surfaces exhibit excellent selectivity, while repeated cycles of hybridization and denaturation in urea show good stability. These results demonstrate that photochemical functionalization can be used as an attractive starting point for interfacing molecular and biomolecular systems with GaN and other compound semiconductors.

  1. Biomolecular detection at ssDNA-conjugated nanoparticles by nano-impact electrochemistry.

    Science.gov (United States)

    Karimi, Anahita; Hayat, Akhtar; Andreescu, Silvana

    2017-01-15

    We describe the use of ssDNA functionalized silver nanoparticle (AgNP) probes for quantitative investigation of biorecognition and real time detection of biomolecular targets using nano-impact electrochemistry. The method is based on measurements of the individual collision events between ssDNA aptamer-functionalized AgNPs and a carbon fiber miroelectrode (CFME). Specific binding events of target analyte induced collision frequency changes enabling ultrasensitive detection of the aptamer target in a single step. These changes are assigned to the surface coverage of the NP by the ssDNA aptamers and subsequent conformational changes of the aptamer probe which affect the electron transfer between the NP and the electrode surface. The method enables sensitive and selective detection of ochratoxin A (OTA), chosen here as a model target, with a limit of detection of 0.05nM and a relative standard deviation of 4.9%. The study provides a means of characterizing bioconjugation of AgNPs with aptamers and assessing biomolecular recognition events with high sensitivity and without the use of exogenous reagents or enzyme amplification steps. This methodology can be broadly applicable to other bioconjugated systems, biosensing and related bioanalytical applications.

  2. Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR

    Science.gov (United States)

    Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio

    2016-03-01

    A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40 s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5 mm NMR tubes. All these ingredients - particularly the ⩾3000× 1H polarization enhancements over 11.7 T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.

  3. The detection of specific biomolecular interactions with micro-Hall magnetic sensors

    Science.gov (United States)

    Manandhar, Pradeep; Chen, Kan-Sheng; Aledealat, Khaled; Mihajlović, Goran; Yun, C. Steven; Field, Mark; Sullivan, Gerard J.; Strouse, Geoffrey F.; Bryant Chase, P.; von Molnár, Stephan; Xiong, Peng

    2009-09-01

    The detection of reagent-free specific biomolecular interactions through sensing of nanoscopic magnetic labels provides one of the most promising routes to biosensing with solid-state devices. In particular, Hall sensors based on semiconductor heterostructures have shown exceptional magnetic moment sensitivity over a large dynamic field range suitable for magnetic biosensing using superparamagnetic labels. Here we demonstrate the capability of such micro-Hall sensors to detect specific molecular binding using biotin-streptavidin as a model system. We apply dip-pen nanolithography to selectively biotinylate the active areas of InAs micro-Hall devices with nanoscale precision. Specific binding of complementarily functionalized streptavidin-coated superparamagnetic beads to the Hall crosses occurs via molecular recognition, and magnetic detection of the assembled beads is achieved at room temperature using phase sensitive micro-Hall magnetometry. The experiment constitutes the first unambiguous demonstration of magnetic detection of specific biomolecular interactions with semiconductor micro-Hall sensors, and the selective molecular functionalization and resulting localized bead assembly demonstrate the possibility of multiplexed sensing of multiple target molecules using a single device with an array of micro-Hall sensors.

  4. Single-Molecule Pull-down FRET (SiMPull-FRET) to dissect the mechanisms of biomolecular machines

    Science.gov (United States)

    Kahlscheuer, Matthew L.; Widom, Julia; Walter, Nils G.

    2016-01-01

    Spliceosomes are multi-megadalton RNA-protein complexes responsible for the faithful removal of non-coding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition and versatile structural dynamics. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues towards studying the mechanisms of biomolecular machines isolated directly from complex biological specimens such as cell extracts. Here we detail the general steps for using prism-based total internal reflection fluorescence (TIRF) microscopy in exemplary single molecule pull-down FRET (SiMPull-FRET) studies of the yeast spliceosome and discuss the broad application potential of this technique. PMID:26068753

  5. Thermo-responsive cell culture carriers based on poly(vinyl methyl ether)—the effect of biomolecular ligands to balance cell adhesion and stimulated detachment

    Science.gov (United States)

    Teichmann, Juliane; Nitschke, Mirko; Pette, Dagmar; Valtink, Monika; Gramm, Stefan; Härtel, Frauke V.; Noll, Thomas; Funk, Richard H. W.; Engelmann, Katrin; Werner, Carsten

    2015-08-01

    Two established material systems for thermally stimulated detachment of adherent cells were combined in a cross-linked polymer blend to merge favorable properties. Through this approach poly(N-isopropylacrylamide) (PNiPAAm) with its superior switching characteristic was paired with a poly(vinyl methyl ether)-based composition that allows adjusting physico-chemical and biomolecular properties in a wide range. Beyond pure PNiPAAm, the proposed thermo-responsive coating provides thickness, stiffness and swelling behavior, as well as an apposite density of reactive sites for biomolecular functionalization, as effective tuning parameters to meet specific requirements of a particular cell type regarding initial adhesion and ease of detachment. To illustrate the strength of this approach, the novel cell culture carrier was applied to generate transplantable sheets of human corneal endothelial cells (HCEC). Sheets were grown, detached, and transferred onto planar targets. Cell morphology, viability and functionality were analyzed by immunocytochemistry and determination of transepithelial electrical resistance (TEER) before and after sheet detachment and transfer. HCEC layers showed regular morphology with appropriate TEER. Cells were positive for function-associated marker proteins ZO-1, Na+/K+-ATPase, and paxillin, and extracellular matrix proteins fibronectin, laminin and collagen type IV before and after transfer. Sheet detachment and transfer did not impair cell viability. Subsequently, a potential application in ophthalmology was demonstrated by transplantation onto de-endothelialized porcine corneas in vitro. The novel thermo-responsive cell culture carrier facilitates the generation and transfer of functional HCEC sheets. This paves the way to generate tissue engineered human corneal endothelium as an alternative transplant source for endothelial keratoplasty.

  6. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations.

    Science.gov (United States)

    Shen, Lin; Hu, Hao

    2014-06-10

    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  7. Utilizing plasma physics to create biomolecular movies

    Energy Technology Data Exchange (ETDEWEB)

    Hau-Riege, S [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2015-07-24

    In spring of 2000, the LCLS Scientific Advisory Committee selected the top scientific experiments for LCLS. One of the proposed flagship experiments is atomic-resolution three-dimensional structure determination of isolated biolgical macromolecules and particles, with the ultimate goal of obtaining molecular (snapshot) movies. The key enabling insight was that radiation damage may be overcome by using x-ray pulses that are shorter than the time it takes for damage to manifest itself.

  8. Condutância molecular e biomolecular

    Directory of Open Access Journals (Sweden)

    Gama A. Arnóbio S. da

    2000-01-01

    Full Text Available The concept of molecular conductance is discussed in terms of the propagation of an electronic interaction, between electron donor and acceptor groups, through the bonds of a molecular structure where these groups are embedded. The electronic interaction propagation is described by a Green's function matrix element, in a donor-bridge-acceptor molecular system reduced to a two-level representation.

  9. Advances in modeling of biomolecular interactions

    Institute of Scientific and Technical Information of China (English)

    Cong-zhongCAI; Ze-rongLI; Wan-luWANG; Yu-zongCHEN

    2004-01-01

    Modeling of molecular interactions is increasingly used in life science research and biotechnology development.Examples are computer aided drug design, prediction of protein interactions with other molecules, and simulation of networks of biomolecules in a particular process in human body. This article reviews recent progress in the related fields and provides a brief overview on the methods used in molecular modeling of biological systems.

  10. 21 CFR 864.7340 - Fibrinogen determination system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Fibrinogen determination system. 864.7340 Section... Fibrinogen determination system. (a) Identification. A fibrinogen determination system is a device that consists of the instruments, reagents, standards, and controls used to determine the fibrinogen levels...

  11. Scanning probe and optical tweezer investigations of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rigby-Singleton, Shellie

    2002-07-01

    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located {approx}0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin

  12. Thermal coupling at aqueous and biomolecular interfaces

    Science.gov (United States)

    Shenogina, Natalia B.

    Heat flow in the materials with nanoscopic features is dominated by thermal properties of the interfaces. While thermal properties of the solid-solid and solid-liquid interfaces are well studied, research of the thermal transport properties across soft (liquid-liquid) interfaces is very limited. Such interfaces are, however, plentiful in biological systems. In such systems the temperature control is of a great importance, because biochemical reactions, conformation of biomolecules as well as processes in biological cells and membranes have strong temperature sensitivity. The critical ingredient to temperature control in biological systems is the understanding of heat flow and thermal coupling across soft interfaces. To investigate heat transfer across biological and aqueous interfaces we chose to study a number of soft interfacial systems by means of molecular dynamic simulations. One of the interfaces under our investigation is the interface between protein (specifically green fluorescent protein) and water. Using this model we concentrated on the importance of vibrational frequency on coupling between water and proteins, and on significant differences between the roles of low and high frequency vibrations. Our thermal interfacial analysis allowed us to shed new light on to the issue of protein to water slaving, i.e., the concept of water controlling protein dynamics. Considering that the surface of the protein is composed of a complicated mixture of the hydrophobic and hydrophilic domains, to systematically explore the role of interfacial interactions we studied less complicated models with homogenous interfaces whith interfacial chemistry that could be changed in a controlled manner. We demonstrated that thermal transport measurements can be used to probe interfacial environments and to quantify interfacial bonding strength. Such ability provides a unique opportunity to characterize a variety of interfaces, which can be difficult to achieve with more direct

  13. Biomolecular transport and separation in nanotubular networks.

    Energy Technology Data Exchange (ETDEWEB)

    Stachowiak, Jeanne C.; Stevens, Mark Jackson (Sandia National Laboratories, Albuquerque, NM); Robinson, David B.; Branda, Steven S.; Zendejas, Frank; Meagher, Robert J.; Sasaki, Darryl Yoshio; Bachand, George David (Sandia National Laboratories, Albuquerque, NM); Hayden, Carl C.; Sinha, Anupama; Abate, Elisa; Wang, Julia; Carroll-Portillo, Amanda (Sandia National Laboratories, Albuquerque, NM); Liu, Haiqing (Sandia National Laboratories, Albuquerque, NM)

    2010-09-01

    Cell membranes are dynamic substrates that achieve a diverse array of functions through multi-scale reconfigurations. We explore the morphological changes that occur upon protein interaction to model membrane systems that induce deformation of their planar structure to yield nanotube assemblies. In the two examples shown in this report we will describe the use of membrane adhesion and particle trajectory to form lipid nanotubes via mechanical stretching, and protein adsorption onto domains and the induction of membrane curvature through steric pressure. Through this work the relationship between membrane bending rigidity, protein affinity, and line tension of phase separated structures were examined and their relationship in biological membranes explored.

  14. Hydrogen Production from Water by Photosynthesis System I for Use as Fuel in Energy Conversion Devices (a.k.a. Understanding Photosystem I as a Biomolecular Reactor for Energy Conversion)

    Science.gov (United States)

    2014-04-01

    Hydrogen Production from Water by Photosynthesis System I for Use as Fuel in Energy Conversion Devices (a.k.a. Understanding Photosystem I as...Laboratory Adelphi, MD 20783-1197 ARL-TR-6904 April 2014 Hydrogen Production from Water by Photosynthesis System I for Use as Fuel in Energy...Final 3. DATES COVERED (From - To) 10/1/2010–10/1/2013 4. TITLE AND SUBTITLE Hydrogen Production from Water by Photosynthesis System I for Use as Fuel

  15. Programming biomolecular self-assembly pathways.

    Science.gov (United States)

    Yin, Peng; Choi, Harry M T; Calvert, Colby R; Pierce, Niles A

    2008-01-17

    In nature, self-assembling and disassembling complexes of proteins and nucleic acids bound to a variety of ligands perform intricate and diverse dynamic functions. In contrast, attempts to rationally encode structure and function into synthetic amino acid and nucleic acid sequences have largely focused on engineering molecules that self-assemble into prescribed target structures, rather than on engineering transient system dynamics. To design systems that perform dynamic functions without human intervention, it is necessary to encode within the biopolymer sequences the reaction pathways by which self-assembly occurs. Nucleic acids show promise as a design medium for engineering dynamic functions, including catalytic hybridization, triggered self-assembly and molecular computation. Here, we program diverse molecular self-assembly and disassembly pathways using a 'reaction graph' abstraction to specify complementarity relationships between modular domains in a versatile DNA hairpin motif. Molecular programs are executed for a variety of dynamic functions: catalytic formation of branched junctions, autocatalytic duplex formation by a cross-catalytic circuit, nucleated dendritic growth of a binary molecular 'tree', and autonomous locomotion of a bipedal walker.

  16. Biomolecular papain thin films grown by matrix assisted and conventional pulsed laser deposition: A comparative study

    Science.gov (United States)

    György, E.; Pérez del Pino, A.; Sauthier, G.; Figueras, A.

    2009-12-01

    Biomolecular papain thin films were grown both by matrix assisted pulsed laser evaporation (MAPLE) and conventional pulsed laser deposition (PLD) techniques with the aid of an UV KrF∗ (λ =248 nm, τFWHM≅20 ns) excimer laser source. For the MAPLE experiments the targets submitted to laser radiation consisted on frozen composites obtained by dissolving the biomaterial powder in distilled water at 10 wt % concentration. Conventional pressed biomaterial powder targets were used in the PLD experiments. The surface morphology of the obtained thin films was studied by atomic force microscopy and their structure and composition were investigated by Fourier transform infrared spectroscopy. The possible physical mechanisms implied in the ablation processes of the two techniques, under comparable experimental conditions were identified. The results showed that the growth mode, surface morphology as well as structure of the deposited biomaterial thin films are determined both by the incident laser fluence value as well as target preparation procedure.

  17. Computer programming and biomolecular structure studies: A step beyond internet bioinformatics.

    Science.gov (United States)

    Likić, Vladimir A

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled Biomolecular Structure and Bioinformatics. Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics approach that relies on access to the Internet and biological databases. This was an ambitious approach considering that the students mostly had a biological background. There were also time constraints of eight lectures in total and two accompanying practical sessions. The main challenge was that students had to be introduced to computer programming from a beginner level and in a short time provided with enough knowledge to independently solve a simple bioinformatics problem. This was accomplished with a problem directly relevant to the rest of the subject, concerned with the structure-function relationships and experimental techniques for the determination of macromolecular structure.

  18. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Guowei; Baker, Nathan A.

    2016-11-11

    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In these approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.

  19. Knowledge based cluster ensemble for cancer discovery from biomolecular data.

    Science.gov (United States)

    Yu, Zhiwen; Wongb, Hau-San; You, Jane; Yang, Qinmin; Liao, Hongying

    2011-06-01

    The adoption of microarray techniques in biological and medical research provides a new way for cancer diagnosis and treatment. In order to perform successful diagnosis and treatment of cancer, discovering and classifying cancer types correctly is essential. Class discovery is one of the most important tasks in cancer classification using biomolecular data. Most of the existing works adopt single clustering algorithms to perform class discovery from biomolecular data. However, single clustering algorithms have limitations, which include a lack of robustness, stability, and accuracy. In this paper, we propose a new cluster ensemble approach called knowledge based cluster ensemble (KCE) which incorporates the prior knowledge of the data sets into the cluster ensemble framework. Specifically, KCE represents the prior knowledge of a data set in the form of pairwise constraints. Then, the spectral clustering algorithm (SC) is adopted to generate a set of clustering solutions. Next, KCE transforms pairwise constraints into confidence factors for these clustering solutions. After that, a consensus matrix is constructed by considering all the clustering solutions and their corresponding confidence factors. The final clustering result is obtained by partitioning the consensus matrix. Comparison with single clustering algorithms and conventional cluster ensemble approaches, knowledge based cluster ensemble approaches are more robust, stable and accurate. The experiments on cancer data sets show that: 1) KCE works well on these data sets; 2) KCE not only outperforms most of the state-of-the-art single clustering algorithms, but also outperforms most of the state-of-the-art cluster ensemble approaches.

  20. Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

    Directory of Open Access Journals (Sweden)

    Cornelia Meinert

    2010-05-01

    Full Text Available Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

  1. Programming in Biomolecular Computation: Programs, Self-Interpretation and Visualisation

    Directory of Open Access Journals (Sweden)

    J.G. Simonsen

    2011-01-01

    Full Text Available Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm; it is also uniform: new ``hardware'' is not needed to solve new problems; and (last but not least it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient.

  2. Advances in biomolecular surface meshing and its applications to mathematical modeling

    Institute of Scientific and Technical Information of China (English)

    CHEN MinXin; LU BenZhuo

    2013-01-01

    In the field of molecular modeling and simulation,molecular surface meshes are necessary for many problems,such as molecular structure visualization and analysis,docking problem and implicit solvent modeling and simulation.Recently,with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation,providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure.In this review,we summarize recent works on this issue.First,various definitions of molecular surfaces and corresponding meshing methods are introduced.Second,our recent meshing tool,TMSmesh,and its performances are presented.Finally,we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM).

  3. Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs

    CERN Document Server

    Yokota, Rio; Bardhan, Jaydeep P; Knepley, Matthew G; Barba, L A

    2010-01-01

    We present simulations of biomolecular electrostatics at a scale not reached before, thanks to both algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. Computational experiments are presented simulating the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of the problems, which models over 20 million atoms and has more than six billion unknowns, one iteration step requires only a few minutes on 512 GPU nodes. We achieved a sustained performance of 34.6TFlops for the entire BEM calculation. We are currently adapting our solver to model the linearized ...

  4. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

    CERN Document Server

    Privman, Vladimir; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny

    2010-01-01

    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved...

  5. Insights into cancer severity from biomolecular interaction mechanisms

    Science.gov (United States)

    Raimondi, Francesco; Singh, Gurdeep; Betts, Matthew J.; Apic, Gordana; Vukotic, Ranka; Andreone, Pietro; Stein, Lincoln; Russell, Robert B.

    2016-01-01

    To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or –nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes. Over half of these interfaces involve protein-small-molecule interactions highlighting their overall importance in cancer. We found distinct differences in the predominance of perturbed interfaces between cancers and histological subtypes and presence or absence of certain interfaces appears to correlate with cancer severity. PMID:27698488

  6. Simulation of Parallel Logical Operations with Biomolecular Computing

    Directory of Open Access Journals (Sweden)

    Mahnaz Kadkhoda

    2008-01-01

    Full Text Available Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circuits. The contribution of this paper is that the proposed algorithm has been implemented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature. Thus, the proposed algorithm is much easier to implement in the laboratory.

  7. Structure and Interactions of Isolated Biomolecular Building Blocks.

    Science.gov (United States)

    de Vries, Mattanjah

    2006-03-01

    We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing.

  8. Orientation of biomolecular assemblies in a microfluidic jet

    Energy Technology Data Exchange (ETDEWEB)

    Priebe, M; Kalbfleisch, S; Tolkiehn, M; Salditt, T [Institut fuer Roentgenphysik, Universitaet Goettingen, Goettingen (Germany); Koester, S [Courant Research Centre Nano-Spectroscopy and X-Ray Imaging, Universitaet Goettingen, Goettingen (Germany); Abel, B [Institut fuer Physikalische Chemie, Universitaet Goettingen, Goettingen (Germany); Davies, R J, E-mail: tsalditt@gwdg.d [ID13, ESRF, Grenoble (France)

    2010-04-15

    We have investigated multilamellar lipid assemblies in a microfluidic jet, operating at high shear rates of the order of 10{sup 7} s{sup -1}. Compared to classical Couette cells or rheometers, the shear rate was increased by at least 2-3 orders of magnitude, and the sample volume was scaled down correspondingly. At the same time, the jet is characterized by high extensional stress due to elongational flow. A focused synchrotron x-ray beam was used to measure the structure and orientation of the lipid assemblies in the jet. The diffraction patterns indicate conventional multilamellar phases, aligned with the membrane normals oriented along the velocity gradient of the jet. The results indicate that the setup may be well suited for coherent diffractive imaging of oriented biomolecular assemblies and macromolecules at the future x-ray free electron laser (XFEL) sources.

  9. Ion irradiation and biomolecular radiation damage II. Indirect effect

    CERN Document Server

    Wang, Wei; Su, Wenhui

    2010-01-01

    It has been reported that damage of genome in a living cell by ionizing radiation is about one-third direct and two-thirds indirect. The former which has been introduced in our last paper, concerns direct energy deposition and ionizing reactions in the biomolecules; the latter results from radiation induced reactive species (mainly radicals) in the medium (mainly water) surrounding the biomolecules. In this review, a short description of ion implantation induced radical formation in water is presented. Then we summarize the aqueous radical reaction chemistry of DNA, protein and their components, followed by a brief introduction of biomolecular damage induced by secondary particles (ions and electron). Some downstream biological effects are also discussed.

  10. Hybrid organic semiconductor lasers for bio-molecular sensing.

    Science.gov (United States)

    Haughey, Anne-Marie; Foucher, Caroline; Guilhabert, Benoit; Kanibolotsky, Alexander L; Skabara, Peter J; Burley, Glenn; Dawson, Martin D; Laurand, Nicolas

    2014-01-01

    Bio-functionalised luminescent organic semiconductors are attractive for biophotonics because they can act as efficient laser materials while simultaneously interacting with molecules. In this paper, we present and discuss a laser biosensor platform that utilises a gain layer made of such an organic semiconductor material. The simple structure of the sensor and its operation principle are described. Nanolayer detection is shown experimentally and analysed theoretically in order to assess the potential and the limits of the biosensor. The advantage conferred by the organic semiconductor is explained, and comparisons to laser sensors using alternative dye-doped materials are made. Specific biomolecular sensing is demonstrated, and routes to functionalisation with nucleic acid probes, and future developments opened up by this achievement, are highlighted. Finally, attractive formats for sensing applications are mentioned, as well as colloidal quantum dots, which in the future could be used in conjunction with organic semiconductors.

  11. Application of isothermal titration calorimetry for characterizing thermodynamic parameters of biomolecular interactions: peptide self-assembly and protein adsorption case studies.

    Science.gov (United States)

    Kabiri, Maryam; Unsworth, Larry D

    2014-10-13

    The complex nature of macromolecular interactions usually makes it very hard to identify the molecular-level mechanisms that ultimately dictate the result of these interactions. This is especially evident in the case of biological systems, where the complex interaction of molecules in various situations may be responsible for driving biomolecular interactions themselves but also has a broader effect at the cell and/or tissue level. This review will endeavor to further the understanding of biomolecular interactions utilizing the isothermal titration calorimetry (ITC) technique for thermodynamic characterization of two extremely important biomaterial systems, viz., peptide self-assembly and nonfouling polymer-modified surfaces. The advantages and shortcomings of this technique will be presented along with a thorough review of the recent application of ITC to these two areas. Furthermore, the controversies associated with the enthalpy-entropy compensation effect as well as thermodynamic equilibrium state for such interactions will be discussed.

  12. The allostery landscape: quantifying thermodynamic couplings in biomolecular systems

    CERN Document Server

    Cuendet, Michel A; LeVine, Michael V

    2016-01-01

    Allostery plays a fundament role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables is not a single number, but instead a two-dimensional thermodynamic coupling function that is directly related to the mutual information from information theory and the copula density function from probability theory. On this basis, we demonstrate how to quantify the contribution of specific energy terms to this thermodynamic coupling function, enabling a decomposition that reveals the mechanism of allostery. We illustrate the thermodynamic coupling function and its use by showing how allosteric coupling in the alanine dipeptide molecule contributes to the overall shape of the {\\Phi}/{\\Psi} free energy surface, and by identifying the interactions that are necessary for this coupling.

  13. An Advanced Platform for Biomolecular Detection and Analysis Systems

    Science.gov (United States)

    2005-02-01

    11 Figure 1.16. Cell-gel fabrication shows a microgel cylinder (a) is polymerized in a microchanel. Fatty acid chains (b) are...Figure 1.16. Figure 1.16. Cell-gel fabrication shows a microgel cylinder (a) is polymerized in a microchanel. Fatty acid chains (b) are covalently linked...the modified microgel (µgel) was exposed to a basic solution (which would normally cause the hydrogel to swell), and the µgel diameter was measured at

  14. Engineered Bio-Molecular Nano-Devices/Systems

    Science.gov (United States)

    2009-03-01

    sharpened Pt microwire into a glass capillary, followed by polishing the glass until a nanometer-sized metal disk is exposed. Complete removal of the...to oligomerize the protein in the presence of rabbit blood cells was not pursued as this requires specific medical capabilities that were not... Medical Center 1750 W. Harrison St. Chicago, IL 60612 Dr. Robert Eisenberg Dr. John Tang 96 of 100 MOLDICE Final Report Contract FA9550-06-C

  15. Nanomechanical force transducers for biomolecular and intracellular measurements: is there room to shrink and why do it?

    Science.gov (United States)

    Sirbuly, Donald J; Friddle, Raymond W; Villanueva, Joshua; Huang, Qian

    2015-02-01

    Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.

  16. Determination of Parameters of PV Concentrating System With Heliostat

    Science.gov (United States)

    Vardanyan, R.; Norsoyan, A.; Dallakyan, V.

    2010-10-01

    The structure of PV concentrating system with heliostat is analyzed. The mathematical model of system consisting of PV concentrating module and heliostat is developed. With the use of developed mathematical model the optimal parameters of the system are determined. The results of this work can be used during the design of PV concentrating systems with heliostats.

  17. The evolution of sex ratios and sex-determining systems

    NARCIS (Netherlands)

    Uller, Tobias; Pen, Ido; Wapstra, Erik; Beukeboom, Leo W.; Komdeur, Jan

    2007-01-01

    Sex determination is a fundamental process governed by diverse mechanisms. Sex ratio selection is commonly implicated in the evolution of sex-determining systems, although formal models are rare. Here, we argue that, although sex ratio selection can induce shifts in sex determination, genomic confli

  18. Determining expected behaviour of fraudsters for a continuous audit system

    Directory of Open Access Journals (Sweden)

    Mathew A. Thomas

    2012-06-01

    Full Text Available This research attempts to determine the behaviour of fraudsters in a continuous audit system where the fraudsters have multiple options for committing fraud. The system is modelled as a Continuous Time Markov Chain where the state changes are caused by the fraudster's actions. The model uses a dynamic game with probabilistic transitions to determine the expected behaviour of the fraudster.

  19. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  20. Determination of thickness and density of a wet multilayer polymer system with sub-nanometer resolution by means of a dual polarization silicon-on-insulator microring

    Science.gov (United States)

    Hoste, J.-W.; De Geest, Bruno G.; Bienstman, Peter

    2015-03-01

    Determination of both thickness and refractive index of a thin biomolecular or polymer layer in wet conditions is a task not easily performed. Available tools such as XPS, AFM, ellipsometry and integrated photonic sensors often have difficulties with the native wet condition of said agents-under-test, perform poorly in the sub-5 nm regime or do not determine both characteristics in an absolute simultaneous way. The thickness of a multilayer system is often determined by averaging over a large amount of layers, obscuring details of the individual layers. Even more, the interesting behavior of the first bound layers can be covered in noise or assumptions might be made on either thickness or refractive index in order to determine the other. To demonstrate a solution to these problems, a silicon-on-insulator (SOI) microring is used to study the adsorption of a bilayer polymer system on the silicon surface of the ring. To achieve this, the microring is simultaneously excited with TE and TM polarized light and by tracking the shifts of both resonant wavelengths, the refractive index and the thickness of the adsorbed layer can be determined with a resolution on thickness smaller than 0.1 nm and a resolution on refractive index smaller than 0.01 RIU. An adhesive polyethyleneimine (PEI) layer is adsorbed to the surface, followed by the adsorption of poly(sodium-4-styrene sulfonate) (PSS) and poly(allylamine) hydrochloride (PAH). This high-resolution performance in wet conditions with the added benefits of the SOI microring platform such as low cost and multiplexibility make for a powerful tool to analyze thin layer systems, which is promising to research binding conformation of proteins as well.

  1. Attitude Determination Error Analysis System (ADEAS) mathematical specifications document

    Science.gov (United States)

    Nicholson, Mark; Markley, F.; Seidewitz, E.

    1988-01-01

    The mathematical specifications of Release 4.0 of the Attitude Determination Error Analysis System (ADEAS), which provides a general-purpose linear error analysis capability for various spacecraft attitude geometries and determination processes, are presented. The analytical basis of the system is presented. The analytical basis of the system is presented, and detailed equations are provided for both three-axis-stabilized and spin-stabilized attitude sensor models.

  2. [Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Implications for pathology].

    Science.gov (United States)

    Viertler, C; Zatloukal, K

    2008-11-01

    High quality human biological samples (e.g. blood, tissue or DNA) with associated, well documented clinical and research data are key resources for advancement of life sciences, biotechnology, clinical medicine, drug development and also molecular pathology. Millions of samples of diseased tissues have been collected in the context of routine histopathological diagnosis and are stored in the archives of hospitals and institutes of pathology. A concerted effort is necessary to overcome the current fragmentation of the European biobanking community in order to tap the full research potential of existing biobanks. A pan-European research infrastructure for biobanking and biomolecular resources (BBMRI) is currently in its planning phase. The mission is to link and provide access to local biobanks of different formats, including tissue collections, harmonize standards, establish operational procedures which properly consider ethical, legal, societal aspects, and to secure sustainable funding. Pathology plays a key role in development and administration of tissue banks and is, thus, a major partner for collaboration, expertise and construction of this pan-European research infrastructure.

  3. Biomolecular Evidence of Silk from 8,500 Years Ago.

    Science.gov (United States)

    Gong, Yuxuan; Li, Li; Gong, Decai; Yin, Hao; Zhang, Juzhong

    2016-01-01

    Pottery, bone implements, and stone tools are routinely found at Neolithic sites. However, the integrity of textiles or silk is susceptible to degradation, and it is therefore very difficult for such materials to be preserved for 8,000 years. Although previous studies have provided important evidence of the emergence of weaving skills and tools, such as figuline spinning wheels and osseous lamellas with traces of filament winding, there is a lack of direct evidence proving the existence of silk. In this paper, we explored evidence of prehistoric silk fibroin through the analysis of soil samples collected from three tombs at the Neolithic site of Jiahu. Mass spectrometry was employed and integrated with proteomics to characterize the key peptides of silk fibroin. The direct biomolecular evidence reported here showed the existence of prehistoric silk fibroin, which was found in 8,500-year-old tombs. Rough weaving tools and bone needles were also excavated, indicating the possibility that the Jiahu residents may possess the basic weaving and sewing skills in making textile. This finding may advance the study of the history of silk, and the civilization of the Neolithic Age.

  4. Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions.

    Science.gov (United States)

    Seidel, Susanne A I; Dijkman, Patricia M; Lea, Wendy A; van den Bogaart, Geert; Jerabek-Willemsen, Moran; Lazic, Ana; Joseph, Jeremiah S; Srinivasan, Prakash; Baaske, Philipp; Simeonov, Anton; Katritch, Ilia; Melo, Fernando A; Ladbury, John E; Schreiber, Gideon; Watts, Anthony; Braun, Dieter; Duhr, Stefan

    2013-03-01

    Microscale thermophoresis (MST) allows for quantitative analysis of protein interactions in free solution and with low sample consumption. The technique is based on thermophoresis, the directed motion of molecules in temperature gradients. Thermophoresis is highly sensitive to all types of binding-induced changes of molecular properties, be it in size, charge, hydration shell or conformation. In an all-optical approach, an infrared laser is used for local heating, and molecule mobility in the temperature gradient is analyzed via fluorescence. In standard MST one binding partner is fluorescently labeled. However, MST can also be performed label-free by exploiting intrinsic protein UV-fluorescence. Despite the high molecular weight ratio, the interaction of small molecules and peptides with proteins is readily accessible by MST. Furthermore, MST assays are highly adaptable to fit to the diverse requirements of different biomolecules, such as membrane proteins to be stabilized in solution. The type of buffer and additives can be chosen freely. Measuring is even possible in complex bioliquids like cell lysate allowing close to in vivo conditions without sample purification. Binding modes that are quantifiable via MST include dimerization, cooperativity and competition. Thus, its flexibility in assay design qualifies MST for analysis of biomolecular interactions in complex experimental settings, which we herein demonstrate by addressing typically challenging types of binding events from various fields of life science.

  5. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations.

    Science.gov (United States)

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo

    2015-12-15

    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

  6. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays.

    Science.gov (United States)

    Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan

    2016-06-01

    The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays.

  7. Amplified Immunoassay of Human IgG Using Real-time Biomolecular Interaction Analysis (BIA) Technology

    Institute of Scientific and Technical Information of China (English)

    PEI,Ren-Jun(裴仁军); CUI,Xiao-Qiang(崔小强); YANG,Xiu-Rong(杨秀荣); WANG,Er-Kang(汪尔康)

    2002-01-01

    An automated biomolecular interaction analysis instrument (BIAcore) based on surface plasmon resonance (SPR) has been used to determine human immunoglobulin G (IgG) in real time. Polyclonal anti-human IgG antibody was covalently immobilized to a carboxymethyldextran-modified gold film surface. The samples of human IgG prepared in HBS buffer were poured over the immobilized surface. The signal amplification antibody was applied to amplify the response signal. After each measurement, the surface was regenerated with 0.1 mol/L H3PO4. The assay was rapid, requiring only 30 min for antibody immobilization and 20 min for each subsequent process of immune binding, antibody amplification and regeneration. The antibody immobilized surface had good response to human IgG in the range of 0.12-60 nmol/L with a detection limit of 60 pmoL/L. The same antibody immobilized surface could be used for more than 110 cycles of binding, amplificafion and regeneration. The results demonstrate that the sensitivity, specificity and reproducibility of amplified immunoassay using real-time BIA technology are satisfactory.

  8. Biomolecular detection using a metal semiconductor field effect transistor

    Science.gov (United States)

    Estephan, Elias; Saab, Marie-Belle; Buzatu, Petre; Aulombard, Roger; Cuisinier, Frédéric J. G.; Gergely, Csilla; Cloitre, Thierry

    2010-04-01

    In this work, our attention was drawn towards developing affinity-based electrical biosensors, using a MESFET (Metal Semiconductor Field Effect Transistor). Semiconductor (SC) surfaces must be prepared before the incubations with biomolecules. The peptides route was adapted to exceed and bypass the limits revealed by other types of surface modification due to the unwanted unspecific interactions. As these peptides reveal specific recognition of materials, then controlled functionalization can be achieved. Peptides were produced by phage display technology using a library of M13 bacteriophage. After several rounds of bio-panning, the phages presenting affinities for GaAs SC were isolated; the DNA of these specific phages were sequenced, and the peptide with the highest affinity was synthesized and biotinylated. To explore the possibility of electrical detection, the MESFET fabricated with the GaAs SC were used to detect the streptavidin via the biotinylated peptide in the presence of the bovine Serum Albumin. After each surface modification step, the IDS (current between the drain and the source) of the transistor was measured and a decrease in the intensity was detected. Furthermore, fluorescent microscopy was used in order to prove the specificity of this peptide and the specific localisation of biomolecules. In conclusion, the feasibility of producing an electrical biosensor using a MESFET has been demonstrated. Controlled placement, specific localization and detection of biomolecules on a MESFET transistor were achieved without covering the drain and the source. This method of functionalization and detection can be of great utility for biosensing application opening a new way for developing bioFETs (Biomolecular Field-Effect Transistor).

  9. Bases biomoleculares do fotoenvelhecimento Molecular basis of photoaging

    Directory of Open Access Journals (Sweden)

    Suelen Montagner

    2009-07-01

    Full Text Available Com o aumento da expectativa de vida, o estudo do processo de envelhecimento orgânico tem sido estimulado. O envelhecimento da pele, órgão que espelha os sinais do tempo, é processo de deterioração progressiva, tempo-dependente, e pode ser intensificado pela exposição solar, então designado fotoenvelhecimento. O dano das radiações sobre diversas estruturas celulares e cutâneas leva a alterações morfológicas nesses componentes, fruto de modificações biomoleculares. Muitas pesquisas são desenvolvidas com o intuito de combater ou minimizar os efeitos do fotoenvelhecimento, porém a principal estratégia nesse sentido continua sendo a prevenção, só conseguida pelo progressivo desvendar dos mecanismos fisiopatogênicos envolvidos nesse processo.As a result of the increase in life expectancy, the study of the organic process of aging has been stimulated. Skin ageing, which reflects the signs of time, is a time-dependent process of progressive deterioration that can be intensified by sun exposure, which is known as photoaging. The damage of radiation on various cell structures and on the skin results in molecular and morphological changes to these components. Many research studies are performed to try to minimize the effects of photoaging; however, the main strategy to manage it is still prevention, which will only be achieved once we learn about the mechanisms involved in the process.

  10. Toxicity evaluation of PEDOT/biomolecular composites intended for neural communication electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Asplund, M; Thaning, E; Von Holst, H [Division of Neuronic Engineering, School of Technology and Health, Royal Institute of Technology, SE-14152 Huddinge (Sweden); Lundberg, J [Section for Neuroradiology, R2:02 NKK-lab, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Sandberg-Nordqvist, A C [Section of Clinical CNS Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Kostyszyn, B [Center for Hearing and Communication Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, M1:01, SE-171 76 Stockholm (Sweden); Inganaes, O, E-mail: maria.asplund@sth.kth.s [Biomolecular and Organic Electronics, IFM, Linkoeping University, SE-581 83 Linkoeping (Sweden)

    2009-08-15

    Electrodes coated with the conducting polymer poly(3,4-ethylene dioxythiophene) (PEDOT) possess attractive electrochemical properties for stimulation or recording in the nervous system. Biomolecules, added as counter ions in electropolymerization, could further improve the biomaterial properties, eliminating the need for surfactant counter ions in the process. Such PEDOT/biomolecular composites, using heparin or hyaluronic acid, have previously been investigated electrochemically. In the present study, their biocompatibility is evaluated. An agarose overlay assay using L929 fibroblasts, and elution and direct contact tests on human neuroblastoma SH-SY5Y cells are applied to investigate cytotoxicity in vitro. PEDOT:heparin was further evaluated in vivo through polymer-coated implants in rodent cortex. No cytotoxic response was seen to any of the PEDOT materials tested. The examination of cortical tissue exposed to polymer-coated implants showed extensive glial scarring irrespective of implant material (Pt:polymer or Pt). However, quantification of immunological response, through distance measurements from implant site to closest neuron and counting of ED1+ cell density around implant, was comparable to those of platinum controls. These results indicate that PEDOT:heparin surfaces were non-cytotoxic and show no marked difference in immunological response in cortical tissue compared to pure platinum controls.

  11. Affinity analysis for biomolecular interactions based on magneto-optical relaxation measurements

    Science.gov (United States)

    Aurich, Konstanze; Nagel, Stefan; Heister, Elena; Weitschies, Werner

    2008-12-01

    Magneto-optical relaxation measurements of magnetically labelled biomolecules are a promising tool for immunometric analyses. Carcinoembryonic antigen (CEA) and its polyclonal and monoclonal antibodies (anti-CEA) were utilized as a model system for affinity analysis of the interaction between antibody and antigen. For this purpose antibodies were coupled with magnetic nanoparticles (MNPs). Aggregation of these antibody sensors due to interactions with the CEA was observed subsequently by measuring the relaxation time of the birefringence of a transmitted laser beam that occurs in a pulsed magnetic field. A kinetic model of chain-like aggregation developed for these purposes enables the rapid and simple calculation of the kinetic parameters of the underlying protein interaction. From the known antigen concentration and the increase in particle size during the interaction we are able to estimate the unknown parameters with standard methods for the statistical description of stepwise polymerization. This novel affinity analysis was successfully applied for the antigen-antibody interaction described herein and can be applied to other biomolecular interactions. First efforts have been made to establish magneto-optical relaxation measurements in body fluids.

  12. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids.

    Science.gov (United States)

    Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J

    2008-01-01

    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments.

  13. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    CERN Document Server

    2014-01-01

    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  14. Determining MTF of digital detector system with Monte Carlo simulation

    Science.gov (United States)

    Jeong, Eun Seon; Lee, Hyung Won; Nam, Sang Hee

    2005-04-01

    We have designed a detector based on a-Se(amorphous Selenium) and done simulation the detector with Monte Carlo method. We will apply the cascaded linear system theory to determine the MTF for whole detector system. For direct comparison with experiment, we have simulated 139um pixel pitch and used simulated X-ray tube spectrum.

  15. Recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices.

    Science.gov (United States)

    Sasaki, Naoki

    2012-01-01

    AC electrokinetics is a generic term that refers to an induced motion of particles and fluids under nonuniform AC electric fields. The AC electric fields are formed by application of AC voltages to microelectrodes, which can be easily integrated into microfluidic devices by standard microfabrication techniques. Moreover, the magnitude of the motion is large enough to control the mass transfer on the devices. These advantages are attractive for biomolecular analysis on the microfluidic devices, in which the characteristics of small space and microfluidics have been mainly employed. In this review, I describe recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. The applications include fluid pumping and mixing by AC electrokinetic flow, and manipulation of biomolecules such as DNA and proteins by various AC electrokinetic techniques. Future prospects for highly functional biomolecular analysis on microfluidic devices with the aid of AC electrokinetics are also discussed.

  16. Output-input ratio in thermally fluctuating biomolecular machines.

    Science.gov (United States)

    Kurzynski, Michal; Torchala, Mieczyslaw; Chelminiak, Przemyslaw

    2014-01-01

    Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. This makes the description of the enzymatic reaction kinetics in terms of conventional rate constants insufficient. In the steady state, upon taking advantage of the assumption that each reaction proceeds through a single pair (the gate) of transition conformational substates of the enzyme-substrates complex, the degree of coupling between the output and the input reaction fluxes has been expressed in terms of the mean first-passage times on a conformational transition network between the distinguished substates. The theory is confronted with the results of random-walk simulations on the five-dimensional hypercube. The formal proof is given that, for single input and output gates, the output-input degree of coupling cannot exceed unity. As some experiments suggest such exceeding, looking for the conditions for increasing the degree of coupling value over unity challenges the theory. Performed simulations of random walks on several model networks involving more extended gates indicate that the case of the degree of coupling value higher than 1 is realized in a natural way on critical branching trees extended by long-range shortcuts. Such networks are scale-free and display the property of the small world. For short-range shortcuts, the networks are scale-free and fractal, representing a reasonable model for biomolecular machines displaying tight coupling, i.e., the degree of coupling equal exactly to unity. A hypothesis is stated that the protein conformational transition networks, as

  17. Sex determination in flowering plants: papaya as a model system.

    Science.gov (United States)

    Aryal, Rishi; Ming, Ray

    2014-03-01

    Unisexuality in flowering plants evolved from a hermaphrodite ancestor. Transition from hermaphrodite to unisexual flowers has occurred multiple times across the different lineages of the angiosperms. Sexuality in plants is regulated by genetic, epigenetic and physiological mechanisms. The most specialized mechanism of sex determination is sex chromosomes. The sex chromosomes ensure the stable segregation of sexual phenotypes by preventing the recombination of sex determining genes. Despite continuous efforts, sex determining genes of dioecious plants have not yet been cloned. Concerted efforts with various model systems are necessary to understand the complex mechanism of sex determination in plants. Papaya (Carica papaya L.) is a tropical fruit tree with three sex forms, male, hermaphrodite, and female. Sexuality in papaya is determined by an XY chromosome system that is in an early evolutionary stage. The male and hermaphrodite of papaya are controlled by two different types of Y chromosomes: Y and Y(h). Large amounts of information in the area of genetics, genomics, and epigenetics of papaya have been accumulated over the last few decades. Relatively short lifecycle, small genome size, and readily available genetic and genomic resources render papaya an excellent model system to study sex determination and sex chromosomes in flowering plants.

  18. Consumer Preferences Determine Resilience of Ecological-Economic Systems

    Directory of Open Access Journals (Sweden)

    Stefan Baumgärtner

    2011-12-01

    Full Text Available We perform a model analysis to study the origins of limited resilience in coupled ecological-economic systems. We demonstrate that under open access to ecosystems for profit-maximizing harvesting forms, the resilience properties of the system are essentially determined by consumer preferences for ecosystem services. In particular, we show that complementarity and relative importance of ecosystem services in consumption may significantly decrease the resilience of (almost any given state of the system. We conclude that the role of consumer preferences and management institutions is not just to facilitate adaptation to, or transformation of, some natural dynamics of ecosystems. Rather, consumer preferences and management institutions are themselves important determinants of the fundamental dynamic characteristics of coupled ecological-economic systems, such as limited resilience.

  19. Federated nonlinear predictive filtering for the gyroless attitude determination system

    Science.gov (United States)

    Zhang, Lijun; Qian, Shan; Zhang, Shifeng; Cai, Hong

    2016-11-01

    This paper presents a federated nonlinear predictive filter (NPF) for the gyroless attitude determination system with star sensor and Global Positioning System (GPS) sensor. This approach combines the good qualities of both the NPF and federated filter. In order to combine them, the equivalence relationship between the NPF and classical Kalman filter (KF) is demonstrated from algorithm structure and estimation criterion. The main features of this approach include a nonlinear predictive filtering algorithm to estimate uncertain model errors and determine the spacecraft attitude by using attitude kinematics and dynamics, and a federated filtering algorithm to process measurement data from multiple attitude sensors. Moreover, a fault detection and isolation algorithm is applied to the proposed federated NPF to improve the estimation accuracy even when one sensor fails. Numerical examples are given to verify the navigation performance and fault-tolerant performance of the proposed federated nonlinear predictive attitude determination algorithm.

  20. Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors.

    Science.gov (United States)

    Zhmurov, A; Dima, R I; Kholodov, Y; Barsegov, V

    2010-11-01

    Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a C(α)-based coarse-grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP-GPU program). We assessed the computational performance of an end-to-end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ∼90-fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force-extension profiles using experimental pulling speeds (v(f) = 1-10 μm/s) employed in atomic force microscopy and in optical tweezers-based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10-fold increase in v(f). This implies that, to resolve accurately the free energy landscape and to relate the results of single-molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall-clock time for biomolecules of size as large as 10(5) residues using the SOP-GPU package.

  1. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)

    2015-09-01

    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  2. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  3. Biomolecularly capped uniformly sized nanocrystalline materials: glutathione-capped ZnS nanocrystals

    Science.gov (United States)

    Torres-Martínez, Claudia L.; Nguyen, Liem; Kho, Richard; Bae, Weon; Bozhilov, Krassimir; Klimov, Victor; Mehra, Rajesh K.

    1999-09-01

    Micro-organisms such as bacteria and yeasts form CdS to detoxify toxic cadmium ions. Frequently, CdS particles formed in yeasts and bacteria were found to be associated with specific biomolecules. It was later determined that these biomolecules were present at the surface of CdS. This coating caused a restriction in the growth of CdS particles and resulted in the formation of nanometre-sized semiconductors (NCs) that exhibited typical quantum confinement properties. Glutathione and related phytochelatin peptides were shown to be the biomolecules that capped CdS nanocrystallites synthesized by yeasts Candida glabrata and Schizosaccharomyces pombe. Although early studies showed the existence of specific biochemical pathways for the synthesis of biomolecularly capped CdS NCs, these NCs could be formed in vitro under appropriate conditions. We have recently shown that cysteine and cysteine-containing peptides such as glutathione and phytochelatins can be used in vitro to dictate the formation of discrete sizes of CdS and ZnS nanocrystals. We have evolved protocols for the synthesis of ZnS or CdS nanocrystals within a narrow size distribution range. These procedures involve three steps: (1) formation of metallo-complexes of cysteine or cysteine-containing peptides, (2) introduction of stoichiometric amounts of inorganic sulfide into the metallo-complexes to initiate the formation of nanocrystallites and finally (3) size-selective precipitation of NCs with ethanol in the presence of Na+. The resulting NCs were characterized by optical spectroscopy, high-resolution transmission electron microscopy (HRTEM), x-ray diffraction and electron diffraction. HRTEM showed that the diameter of the ZnS-glutathione nanocrystals was 3.45+/-0.5 nm. X-ray diffraction and electron diffraction analyses indicated ZnS-glutathione to be hexagonal. Photocatalytic studies suggest that glutathione-capped ZnS nanocrystals prepared by our procedure are highly efficient in degrading a test model

  4. Determining the Bayesian optimal sampling strategy in a hierarchical system.

    Energy Technology Data Exchange (ETDEWEB)

    Grace, Matthew D.; Ringland, James T.; Boggs, Paul T.; Pebay, Philippe Pierre

    2010-09-01

    Consider a classic hierarchy tree as a basic model of a 'system-of-systems' network, where each node represents a component system (which may itself consist of a set of sub-systems). For this general composite system, we present a technique for computing the optimal testing strategy, which is based on Bayesian decision analysis. In previous work, we developed a Bayesian approach for computing the distribution of the reliability of a system-of-systems structure that uses test data and prior information. This allows for the determination of both an estimate of the reliability and a quantification of confidence in the estimate. Improving the accuracy of the reliability estimate and increasing the corresponding confidence require the collection of additional data. However, testing all possible sub-systems may not be cost-effective, feasible, or even necessary to achieve an improvement in the reliability estimate. To address this sampling issue, we formulate a Bayesian methodology that systematically determines the optimal sampling strategy under specified constraints and costs that will maximally improve the reliability estimate of the composite system, e.g., by reducing the variance of the reliability distribution. This methodology involves calculating the 'Bayes risk of a decision rule' for each available sampling strategy, where risk quantifies the relative effect that each sampling strategy could have on the reliability estimate. A general numerical algorithm is developed and tested using an example multicomponent system. The results show that the procedure scales linearly with the number of components available for testing.

  5. Mixing height determination using remote sensing systems. General remarks

    Energy Technology Data Exchange (ETDEWEB)

    Beyrich, F. [BTU Cottbus, LS Umweltmeteorologie, Cottbus (Germany)

    1997-10-01

    Remote sensing systems can be considered today as a real alternative to classical soundings with respect to the MH (mixing height) determination. They have the basic advantage to allow continuous monitoring of the ABL (atmospheric boundary layer). Some technical issues which limit their operational use at present should be solved in the near future (frequency allocation, eye safety, costs). Taking into account specific operating conditions and the formulated-above requirements of a sounding system to be used for MH determination it becomes obvious that none of the available systems meets all of them, i.e., the `Mixing height-meter` does not exist. Therefore, reliable MH determination under a wide variety of conditions can be achieved only by integrating different instruments into a complex sounding system. The S-profiles provide a suitable data base for MH estimation from all types of remote sensing instruments. The criteria to deduce MH-values from these profiles should consider the structure type and the evolution stage of the ABL as well as the shape of the profiles. A certain kind of harmonization concerning these criteria should be achieved. MH values derived automatically from remote sensing data appear to be not yet reliable enough for direct operational use, they should be in any case critically examined by a trained analyst. Contemporary mathematical methods (wavelet transforms, fuzzy logics) are supposed to allow considerable progress in this field in the near future. (au) 19 refs.

  6. g_contacts: Fast contact search in bio-molecular ensemble data

    Science.gov (United States)

    Blau, Christian; Grubmuller, Helmut

    2013-12-01

    Short-range interatomic interactions govern many bio-molecular processes. Therefore, identifying close interaction partners in ensemble data is an essential task in structural biology and computational biophysics. A contact search can be cast as a typical range search problem for which efficient algorithms have been developed. However, none of those has yet been adapted to the context of macromolecular ensembles, particularly in a molecular dynamics (MD) framework. Here a set-decomposition algorithm is implemented which detects all contacting atoms or residues in maximum O(Nlog(N)) run-time, in contrast to the O(N2) complexity of a brute-force approach. Catalogue identifier: AEQA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEQA_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 8945 No. of bytes in distributed program, including test data, etc.: 981604 Distribution format: tar.gz Programming language: C99. Computer: PC. Operating system: Linux. RAM: ≈Size of input frame Classification: 3, 4.14. External routines: Gromacs 4.6[1] Nature of problem: Finding atoms or residues that are closer to one another than a given cut-off. Solution method: Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets. Running time:≤O(Nlog(N)) References: [1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013).

  7. Determination of autoantibodies to annexin XI in systemic autoimmune diseases

    DEFF Research Database (Denmark)

    Jorgensen, C S; Levantino, G; Houen, Gunnar

    2000-01-01

    Annexin XI, a calcyclin-associated protein, has been shown to be identical to a 56,000 Da antigen recognized by antibodies found in sera from patients suffering from systemic autoimmune diseases. In this work hexahistidine-tagged recombinant annexin XI (His6- rAnn XI) was used as antigen in ELISA...... experiments for determination of autoantibodies to annexin XI in sera of patients with systemic rheumatic autoimmune diseases. Immunoblotting with HeLa cell extract and with His6-rAnn XI as antigen was used for confirmation of positive ELISA results. We found eleven anti-annexin XI positive sera (3.9%) out...... of 282 sera from patients with systemic rheumatic diseases. The highest number of annexin XI positive sera were found in primary antiphospholipid syndrome (3/17), and in subacute lupus erythematosus (1/6), while lower frequencies of positive sera were found in patients with systemic sclerosis (5...

  8. P System antigenic determiners expression in Ascaris lumbricoides

    Directory of Open Access Journals (Sweden)

    Ponce De León Patricia

    2003-01-01

    Full Text Available The P System antigens have been detected in numerous parasites, bacterias and viruses, nevertheless the clinical significance is still unknown. The aim was to study the presence of P1 antigenic determiners in A. lumbricoides extracts by means of the use of 6 different monoclonal antibodies of well-known concentrations and Ig class. We worked with 14 A. lumbricoides extracts. Inhibition Agglutination Test was made in a bromelin enzymatic medium and 4 masculineC temperature. Titre, Score and Sensitivity Parameter were determined for each monoclonal antibody against red cells suspension used as revealing system. Ten extracts inhibited the agglutination of all anti P1 monoclonal antibodies. The 4 remaining extracts only inhibited the agglutination of some of them. It is demonstrated that the extracts have P1 activity. This activity is independent of titre, Score, Sensitivity Parameter, concentration and Ig class and it depends on the epitope at which the monoclonal antibody is directed.

  9. Plant health sensing system for determining nitrogen status in plants

    Science.gov (United States)

    Thomasson, J. A.; Sui, Ruixiu; Read, John J.; Reddy, K. R.

    2004-03-01

    A plant health sensing system was developed for determining nitrogen status in plants. The system consists of a multi-spectral optical sensor and a data-acquisition and processing unit. The optical sensor"s light source provides modulated panchromatic illumination of a plant canopy with light-emitting diodes, and the sensor measures spectral reflectance through optical filters that partition the energy into blue, green, red, and near-infrared wavebands. Spectral reflectance of plants is detected in situ, at the four wavebands, in real time. The data-acquisition and processing unit is based on a single board computer that collects data from the multi-spectral sensor and spatial information from a global positioning system receiver. Spectral reflectance at the selected wavebands is analyzed, with algorithms developed during preliminary work, to determine nitrogen status in plants. The plant health sensing system has been tested primarily in the laboratory and field so far, and promising results have been obtained. This article describes the development, theory of operation, and test results of the plant health sensing system.

  10. DETERMIN LARGE PRIME NUMBERS TO COMPUTE RSA SYSTEM PARAMETERS

    Directory of Open Access Journals (Sweden)

    Ioan Mang

    2008-05-01

    Full Text Available Cryptography, the secret writing, is probably same old as writing itself and has applications in data security insurance. There are cryptosystems where the encipher algorithm can be public. These are public key algorithms. Research on public key algorithms has been concerned with security aspects. The results of this research have induced sufficient confidence to apply public key cryptography a larger scale. The most used and checked public key-based cryptosystem was find by Rivest, Shamir and Adleman, so called RSA system. This paper shows the RSA algorithm. We have realised a program that is able to determine prime numbers with over 100 digits and compute RSA system parameters.

  11. Expert system for determination of fumonisins in corn samples

    Directory of Open Access Journals (Sweden)

    Abramović Biljana F.

    2005-01-01

    Full Text Available An expert system (ES to solve the problem of choosing an optimal procedure for the determination of fumonisins in corn samples was developed, having in mind that these toxins most frequently contaminate this particular cereal. In constructing the ES use was made of the deterministic approach starting from the assumption that the experts in the field have a profound knowledge about the problem in question. The ES knowledge base contains the solutions that have been published in the pertinent literature, as well as some solutions and recommendations, which we have developed and introduced. On the basis of this information, as well as on the basis of the demanded method detection limit, available equipment, chemicals, as well as the time the experimenter has at his disposal for the determination, the ES proposes a procedure for solving the given analytical problem, starting from sampling, preparation of all the necessary solutions, the appropriate apparatus, probe preparation, the mode of determining results, calculation of the results, and provides a survey of all the relevant literature references. The base of ES is a shell, which can work under a variety of Microsoft Windows operating systems. In the development of ES and its adaptation for users who are not familiar with computer techniques, different tools, which operate with Microsoft Windows operating systems, as well as the tools within Microsoft Office are used.

  12. Implementation of a low-cost, commercial orbit determination system

    Science.gov (United States)

    Corrigan, Jim

    1994-11-01

    Traditional satellite and launch control systems have consisted of custom solutions requiring significant development and maintenance costs. These systems have typically been designed to support specific program requirements and are expensive to modify and augment after delivery. The expanding role of space in today's marketplace combined with the increased sophistication and capabilities of modern satellites has created a need for more efficient, lower cost solutions to complete command and control systems. Recent technical advances have resulted in commercial-off-the-shelf products which greatly reduce the complete life-cycle costs associated with satellite launch and control system procurements. System integrators and spacecraft operators have, however, been slow to integrate these commercial based solutions into a comprehensive command and control system. This is due, in part, to a resistance to change and the fact that many available products are unable to effectively communicate with other commercial products. The United States Air Force, responsible for the health and safety of over 84 satellites via its Air Force Satellite Control Network (AFSCN), has embarked on an initiative to prove that commercial products can be used effectively to form a comprehensive command and control system. The initial version of this system is being installed at the Air Force's Center for Research Support (CERES) located at the National Test Facility in Colorado Springs, Colorado. The first stage of this initiative involved the identification of commercial products capable of satisfying each functional element of a command and control system. A significant requirement in this product selection criteria was flexibility and ability to integrate with other available commercial products. This paper discusses the functions and capabilities of the product selected to provide orbit determination functions for this comprehensive command and control system.

  13. Noise simulation system for determining imaging conditions in digital radiography

    Science.gov (United States)

    Tanaka, R.; Ichikawa, K.; Matsubara, K.; Kawashima, H.

    2012-03-01

    Reduction of exposure dose and improvement in image quality can be expected to result from advances in the performance of imaging detectors. We propose a computerized method for determining optimized imaging conditions by use of simulated images. This study was performed to develop a prototype system for image noise and to ensure consistency between the resulting images and actual images. An RQA5 X-ray spectrum was used for determination of input-output characteristics of a flat-panel detector (FPD). The number of incident quantum to the detector per pixel (counts/pixel) was calculated according to the pixel size of the detector and the quantum number in RQA5 determined in IEC6220-1. The relationship among tube current-time product (mAs), exposure dose (C/kg) at the detector surface, the number of incident quanta (counts/pixel), and pixel values measured on the images was addressed, and a conversion function was then created. The images obtained by the FPD was converted into a map of incident quantum numbers and input into random-value generator to simulate image noise. In addition, graphic user interface was developed to observe images with changing image noise and exposure dose levels, which have trade-off relationship. Simulation images provided at different noise levels were compared with actual images obtained by the FPD system. The results indicated that image noise was simulated properly both in objective and subjective evaluation. The present system could allow us to determine necessary dose from image quality and also to estimate image quality from any exposure dose.

  14. Saponification reaction system: a detailed mass transfer coefficient determination.

    Science.gov (United States)

    Pečar, Darja; Goršek, Andreja

    2015-01-01

    The saponification of an aromatic ester with an aqueous sodium hydroxide was studied within a heterogeneous reaction medium in order to determine the overall kinetics of the selected system. The extended thermo-kinetic model was developed compared to the previously used simple one. The reaction rate within a heterogeneous liquid-liquid system incorporates a chemical kinetics term as well as mass transfer between both phases. Chemical rate constant was obtained from experiments within a homogeneous medium, whilst the mass-transfer coefficient was determined separately. The measured thermal profiles were then the bases for determining the overall reaction-rate. This study presents the development of an extended kinetic model for considering mass transfer regarding the saponification of ethyl benzoate with sodium hydroxide within a heterogeneous reaction medium. The time-dependences are presented for the mass transfer coefficient and the interfacial areas at different heterogeneous stages and temperatures. The results indicated an important role of reliable kinetic model, as significant difference in k(L)a product was obtained with extended and simple approach.

  15. DETERMINATION OF EFFICIENCY OF THE CIRCUMFERENTIAL DRAINAGE SYSTEM

    Directory of Open Access Journals (Sweden)

    Maciej Kroll

    2015-11-01

    Full Text Available One of the potential alternatives to improve the stability coefficient for an embankment structure is to flatten the filtration curve. As a result, we obtain lower body forces triggering the potential landslide and more advantageous soil strength parameters, which counteract landslide movements. In the case of waste dumps lowering the phreatic surface of waters is achieved thanks to the construction of auxiliary drainage systems, meeting the guidelines for their safe operation. The aim of this paper is to indicate a method facilitating the determination of the actual position of the phreatic surface within the deposited sediments and the assessment of efficiency of the circumferential drainage system in the waste dump. It was decided in this study to apply cone penetration test CPTU. The CPTU made it possible to measure dissipation of excess water pressure in pores identifying drainage conditions, which were compared with the results of piezometric measurements. The results of these tests made it possible to monitor changes in the position of the depression curve of supernatant waters in dams and to determine the efficiency of the circumferential drainage system.

  16. A simplified electrophoretic system for determining molecular weights of proteins.

    Science.gov (United States)

    Manwell, C

    1977-09-01

    Electrophoresis of 31 different proteins in commercially prepared polyacrylamide gradient gels, Gradipore, yields a linear relationship between a hypothetical limiting pore size (the reciprocal of a limiting gel concentration, GL) and the cube root of the mol.wt., over the range 13 500-9000 000. A regression analysis of these data reveals that 98.6% of all variability in 1/GL is explained by the molecular weight, and this degree of accuracy compares favourably with existing methods for the determination of molecular weight by retardation of mobility in polyacrylamide. This new procedure has the additional advantages that molecular-weight standards can be obtained from readily available body fluids or tissue extracts by localizing enzymes and other proteins by standard histochemical methods, and that the same electrophoretic system can be used in determining molecular weights as is used in routine surveys of populations for individual and species variation in protein heterogeneity.

  17. Determination of a Vapor Compression Refrigeration System Refrigerant Charge

    Institute of Scientific and Technical Information of China (English)

    YangChun-Xin; DangChao-Bin

    1995-01-01

    A physical model is established in this paper to describe the heat transfer and two phase flow of a refrigerant in the evaporator and condenser of a vapor compression refrigeration system.The model in then used to determine the refrigerant charge in vapor compression units.The model is used for a sensitivity analysis to determine the effect that varing design parameters on the refrigerant charge,The model is also used to evaluate the effect of refrigerant charge and the thermal physical properties on the refrigeration cycle,The predicted value of the refigerant charge and experimental data agree well The model and the method presented in this paper could be used to design vapour compression units such as domestic refrigeratirs and air conditioners.

  18. Determinants of bacterial communities in Canadian agroforestry systems.

    Science.gov (United States)

    Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

    2016-06-01

    Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems.

  19. On Determinism in Modal Transition Systems

    DEFF Research Database (Denmark)

    Benes, Nikola; Kretinsky, Jan; Larsen, Kim Guldstrand

    2009-01-01

    with respect to the semantic view based on the sets of the implementations of a given MTS specification. Recent work indicates that some of these limitations might be overcome by considering deterministic systems, which seem to be more manageable but still interesting for several application areas....... In the present article, we provide a comprehensive account of the MTS framework in the deterministic setting. We study a number of problems previously considered on MTS and point out to what extend we can expect better results under the restriction of determinism....

  20. Specificity quantification of biomolecular recognition and its implication for drug discovery

    Science.gov (United States)

    Yan, Zhiqiang; Wang, Jin

    2012-03-01

    Highly efficient and specific biomolecular recognition requires both affinity and specificity. Previous quantitative descriptions of biomolecular recognition were mostly driven by improving the affinity prediction, but lack of quantification of specificity. We developed a novel method SPA (SPecificity and Affinity) based on our funneled energy landscape theory. The strategy is to simultaneously optimize the quantified specificity of the ``native'' protein-ligand complex discriminating against ``non-native'' binding modes and the affinity prediction. The benchmark testing of SPA shows the best performance against 16 other popular scoring functions in industry and academia on both prediction of binding affinity and ``native'' binding pose. For the target COX-2 of nonsteroidal anti-inflammatory drugs, SPA successfully discriminates the drugs from the diversity set, and the selective drugs from non-selective drugs. The remarkable performance demonstrates that SPA has significant potential applications in identifying lead compounds for drug discovery.

  1. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

    2008-01-01

    Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

  2. Constructing Bio-molecular Databases on a DNA-based Computer

    CERN Document Server

    Chang, Weng-Long; Ho,; Guo, Minyi

    2007-01-01

    Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path problem. From [Adleman 1994], it is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer) and a dramatic improvement over existing storage media such as video tape which store information at a density of approximately 1 bit per 1012 cubic nanometers. This paper demonstrates that biological operations can be applied to construct bio-molecular databases where data records in relational tables are encoded as DNA strands. In order to achieve the goal, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases, which include Cartesian product, union, set difference, selection, projection, intersection, join and division. Fu...

  3. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...... non-linear responses with increasing surface concentration. The results from this study support the conventional amphiphilic, triblock model of BSM in the adsorption onto hydrophobic surface from aqueous solution.The biomolecular probe-based approaches employed in this study, however, provided further...

  4. A system dynamics model to determine products mix

    Directory of Open Access Journals (Sweden)

    Mahtab Hajghasem

    2014-02-01

    Full Text Available This paper presents an implementation of system dynamics model to determine appropriate product mix by considering various factors such as labor, materials, overhead, etc. for an Iranian producer of cosmetic and sanitary products. The proposed model of this paper considers three hypotheses including the relationship between product mix and profitability, optimum production capacity and having minimum amount of storage to take advantage of low cost production. The implementation of system dynamics on VENSIM software package has confirmed all three hypotheses of the survey and suggested that in order to reach better mix product, it is necessary to reach optimum production planning, take advantage of all available production capacities and use inventory management techniques.

  5. Initial airworthiness determining the acceptability of new airborne systems

    CERN Document Server

    Gratton, Guy

    2015-01-01

    Designed as an introduction for both advanced students in aerospace engineering and existing aerospace engineers, this book covers both engineering theory and professional practice in establishing the airworthiness of new and modified aircraft. Initial Airworthiness includes information on: ·         how structural, handling, and systems evaluations are carried out; ·         the processes by which safety and fitness for purpose are determined; and ·         the use of both US and European unit systems Covering both civil and military practice and the current regulations and standards across Europe and North America, Initial Airworthiness will give the reader an understanding of how all the major aspects of an aircraft are certified, as well as providing a valuable source of reference for existing practitioners.

  6. A method to determine arc position in ICRF systems

    Energy Technology Data Exchange (ETDEWEB)

    D’Inca, R., E-mail: rodolphe.dinca@ipp.mpg.de [Max-Planck-Institut für Plasmaphysik, EURATOM Association, Garching (Germany); Polozhiy, K.; Eckert, B.; Siegel, G. [Max-Planck-Institut für Plasmaphysik, EURATOM Association, Garching (Germany); Noterdaeme, J.-M. [Max-Planck-Institut für Plasmaphysik, EURATOM Association, Garching (Germany); EESA Department, Gent University (Belgium)

    2013-10-15

    Highlights: ► We show that the voltage noise characteristic of an arc in an ICRF system is due to the propagation and reflections of an electromagnetic pulse emitted by this arc. ► A simplified RF model of an arc in a testbed representative of an ICRF system is developed to see the effect of its location on the voltage noise it emits. ► The model is compared with the results on the testbed for arcs occurring at two locations: one can be determined precisely, the other with a decreased accuracy. -- Abstract: The study of arcs on ICRF systems has mainly focused on the development of fast detectors to detect a breakdown, independently from its position, before they can damage the components [1]. However, the ability to localize an arc is also an important factor: arcs can be the sign of a defect and if they occur at the same location, they give a good indication of the position of this defect without having to use intrusive diagnostics like optical fibers. We present here a method to find the position of arcs based on the analysis of their high-frequency noise. Arcs are indeed fast transient which excite frequencies in the MHz range. The SHAD system reacts on the integral value of this noise signal to detect the development of arcs. But a further investigation of this signal shows detailed features like splittings and chirpings of the frequency peaks which give more information on the source of the breakdown: at its birth, the arc emits a short electromagnetic pulse of several nanoseconds that propagates inside the ICRF system; this pulse is reflected by components like the antenna, the stub tuners or the generators back to the arc thereby changing its boundary conditions. This resonance between the arc and the ICRF system can be measured and the time of propagation of the pulse gives useful data on the position of the breakdown. We have carried out tests on the Manipulator eXPeriment (a testbed to artificially create arcs in a representative ICRF system) and

  7. Parity Violation in Chiral Molecules: From Theory towards Spectroscopic Experiment and the Evolution of Biomolecular Homochirality

    CERN Document Server

    CERN. Geneva

    2016-01-01

    The observation of biomolecular homochirality can be considered as a quasi-fossil of the evolution of life [1], the interpretation of which has been an open question for more than a century, with numerous related hypotheses, but no definitive answers. We shall briefly discuss the current status and the relation to the other two questions. The discovery of parity violation led to important developm...

  8. Accelerated search for biomolecular network models to interpret high-throughput experimental data

    Directory of Open Access Journals (Sweden)

    Sokhansanj Bahrad A

    2007-07-01

    Full Text Available Abstract Background The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control protein expression. Models of biomolecular network structure and dynamics can be inferred from high-throughput measurements of gene and protein expression. We build on our previously developed fuzzy logic method for bridging quantitative and qualitative biological data to address the challenges of noisy, low resolution high-throughput measurements, i.e., from gene expression microarrays. We employ an evolutionary search algorithm to accelerate the search for hypothetical fuzzy biomolecular network models consistent with a biological data set. We also develop a method to estimate the probability of a potential network model fitting a set of data by chance. The resulting metric provides an estimate of both model quality and dataset quality, identifying data that are too noisy to identify meaningful correlations between the measured variables. Results Optimal parameters for the evolutionary search were identified based on artificial data, and the algorithm showed scalable and consistent performance for as many as 150 variables. The method was tested on previously published human cell cycle gene expression microarray data sets. The evolutionary search method was found to converge to the results of exhaustive search. The randomized evolutionary search was able to converge on a set of similar best-fitting network models on different training data sets after 30 generations running 30 models per generation. Consistent results were found regardless of which of the published data sets were used to train or verify the quantitative predictions of the best-fitting models for cell cycle gene dynamics. Conclusion Our results demonstrate the capability of scalable evolutionary search for fuzzy network models to address the problem of inferring models based on complex, noisy biomolecular

  9. Colloid-in-Liquid Crystal Gels that Respond to Biomolecular Interactions

    OpenAIRE

    Agarwal, Ankit; Sidiq, Sumyra; Setia, Shilpa; Bukusoglu, Emre; de Pablo, Juan J.; Pal, Santanu Kumar; Abbott, Nicholas L.

    2013-01-01

    This paper advances the design of stimuli-responsive materials based on colloidal particles dispersed in liquid crystals (LCs). Specifically, we report that thin films of colloid-in-liquid crystal (CLC) gels can undergo easily visualized ordering transitions in response to reversible and irreversible (enzymatic) biomolecular interactions occurring at aqueous interfaces of the gels. In particular, we demonstrate that LC ordering transitions can propagate across the entire thickness of the gels...

  10. Assembly of single wall carbon nanotube-metal nanohybrids using biomolecular components

    Science.gov (United States)

    Kim, Sang Nyon; Slocik, Joseph M.; Naik, Rajesh R.

    2010-08-01

    Biomaterials such as nucleic acids and proteins can be exploited to create higher order structures. The biomolecular components such as DNA and peptides have been used to assemble nanoparticles with high fidelity. Here, we use DNA and peptides, and their preferential interaction with inorganic and carbon nanomaterials to form homogeneous hybrids. The enhanced binding of Pt ions to both DNA and peptide functionalized nanoparticles mediates the assembly of carbon nanotubes functionalized with DNA with peptide coated gold nanoparticles.

  11. Two Axis Pointing System (TAPS) attitude acquisition, determination, and control

    Science.gov (United States)

    Azzolini, John D.; McGlew, David E.

    1990-12-01

    The Two Axis Pointing System (TAPS) is a 2 axis gimbal system designed to provide fine pointing of Space Transportation System (STS) borne instruments. It features center-of-mass instrument mounting and will accommodate instruments of up to 1134 kg (2500 pounds) which fit within a 1.0 by 1.0 by 4.2 meter (40 by 40 by 166 inch) envelope. The TAPS system is controlled by a microcomputer based Control Electronics Assembly (CEA), a Power Distribution Unit (PDU), and a Servo Control Unit (SCU). A DRIRU-II inertial reference unit is used to provide incremental angles for attitude propagation. A Ball Brothers STRAP star tracker is used for attitude acquisition and update. The theory of the TAPS attitude determination and error computation for the Broad Band X-ray Telescope (BBXRT) are described. The attitude acquisition is based upon a 2 star geometric solution. The acquisition theory and quaternion algebra are presented. The attitude control combines classical position, integral and derivative (PID) control with techniques to compensate for coulomb friction (bias torque) and the cable harness crossing the gimbals (spring torque). Also presented is a technique for an adaptive bias torque compensation which adjusts to an ever changing frictional torque environment. The control stability margins are detailed, with the predicted pointing performance, based upon simulation studies. The TAPS user interface, which provides high level operations commands to facilitate science observations, is outlined.

  12. Flight results of a low-cost attitude determination system

    Science.gov (United States)

    Springmann, John C.; Cutler, James W.

    2014-06-01

    This paper presents flight results of the attitude determination system (ADS) flown on the Radio Aurora Explorer (RAX) satellites, RAX-1 and RAX-2, which are CubeSats developed to study space weather. The ADS sensors include commercial-off-the-shelf magnetometers, coarse sun sensors (photodiodes), and a MEMs rate gyroscope. A multiplicative extended Kalman filter is used for attitude estimation. On-orbit calibration was developed and applied to compensate for sensor and alignment errors, and attitude determination accuracies of 0.5° 1-σ have been demonstrated on-orbit. The approach of using low-cost sensors in conjunction with on-orbit calibration, which mitigates the need for pre-flight calibration and high-tolerance alignment during spacecraft assembly, reduces the time and cost associated with the subsystem development, and provides a low-cost solution for modest attitude determination requirements. Although the flight results presented in this paper are from a specific mission, the methods used and lessons learned can be used to maximize the performance of the ADS of any vehicle while minimizing the pre-flight calibration and alignment requirements.

  13. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications.

    Science.gov (United States)

    Yu, Yong; Mok, Beverly Y L; Loh, Xian Jun; Tan, Yen Nee

    2016-08-01

    Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents.

  14. Changes in biomolecular profile in a single nucleolus during cell fixation.

    Science.gov (United States)

    Kuzmin, Andrey N; Pliss, Artem; Prasad, Paras N

    2014-11-01

    Fixation of biological sample is an essential technique applied in order to "freeze" in time the intracellular molecular content. However, fixation induces changes of the cellular molecular structure, which mask physiological distribution of biomolecules and bias interpretation of results. Accurate, sensitive, and comprehensive characterization of changes in biomolecular composition, occurring during fixation, is crucial for proper analysis of experimental data. Here we apply biomolecular component analysis for Raman spectra measured in the same nucleoli of HeLa cells before and after fixation by either formaldehyde solution or by chilled ethanol. It is found that fixation in formaldehyde does not strongly affect the Raman spectra of nucleolar biomolecular components, but may significantly decrease the nucleolar RNA concentration. At the same time, ethanol fixation leads to a proportional increase (up to 40%) in concentrations of nucleolar proteins and RNA, most likely due to cell shrinkage occurring in the presence of coagulant fixative. Ethanol fixation also triggers changes in composition of nucleolar proteome, as indicated by an overall reduction of the α-helical structure of proteins and increase in the concentration of proteins containing the β-sheet conformation. We conclude that cross-linking fixation is a more appropriate protocol for mapping of proteins in situ. At the same time, ethanol fixation is preferential for studies of RNA-containing macromolecules. We supplemented our quantitative Raman spectroscopic measurements with mapping of the protein and lipid macromolecular groups in live and fixed cells using coherent anti-Stokes Raman scattering nonlinear optical imaging.

  15. Application of isothermal titration calorimetry and column chromatography for identification of biomolecular targets.

    Science.gov (United States)

    Zhou, Xingding; Kini, R Manjunatha; Sivaraman, J

    2011-02-01

    This protocol describes a method for identifying unknown target proteins from a mixture of biomolecules for a given drug or a lead compound. This method is based on a combination of chromatography and isothermal titration calorimetry (ITC) where ITC is used as a tracking tool. The first step involves the use of ITC to confirm the binding of ligand to a component in the biomolecular mixture. Subsequently, the biomolecular mixture is fractionated by chromatography, and the binding of the ligand with individual fractions (or subfractions) is verified by ITC. The iteration of chromatographic purification on the fractions combined with ITC results in identifying the target protein. This method is useful when the target protein or ligand is unknown and/or not amenable to labeling, chemical modification or immobilization. This protocol has been successfully used by our team and by others to identify both low-abundance and highly abundant target proteins present in biomolecular mixtures. With this protocol, it takes approximately 3-5 d to identify the target protein from a mixture.

  16. Nanogap biosensors for electrical and label-free detection of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Kyu Kim, Sang; Cho, Hyunmin; Park, Hye-Jung; Kwon, Dohyoung; Min Lee, Jeong; Hyun Chung, Bong, E-mail: chungbh@kribb.re.k [BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, PO Box 115, Yuseong, Daejeon 305-600 (Korea, Republic of)

    2009-11-11

    We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml{sup -1}-100 ng ml{sup -1} at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.

  17. An improved simple polarisable water model for use in biomolecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Bachmann, Stephan J.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich (Switzerland)

    2014-12-14

    The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation.

  18. Digitally determining forest inventory units with an ecological classification system

    Institute of Scientific and Technical Information of China (English)

    TANG Lina; WANG Qingli; Guofan Shao; DAI Limin; WANG Shunzhong; LI Xiufen; XU Dong

    2006-01-01

    Management-level forest resource data in China were obtained with a combination of two forest inventories. However, inconsistencies in the spatial attributes of forest data vary between the two inventory types and between two inventories of the same type. The inconsistencies make it inconvenient for long-term forest management planning with digital technologies. Ecological Land Types (ELTs) and Ecological Land Type Phases (ELTPs) have been mapped in selected forestry regions in northeast China, where important forest industries are located. The boundaries of ELTs are determined by geomorphic conditions, which are quantified by Digital Elevation Models (DEM); ELTPs are classified by overlaying ELTs with forest vegetation data layers that are obtained with both remotely sensed and ground data. The ELTPs represent the divisions of land in terms of both natural and human-induced forest conditions, and therefore they are reliable units for forest inventories and management. This paper introduces a case study for digitally determining forest inventory units in Benxi City, Liaoning Province, northeast China. The general objective of the study was to explain how a compatible forest inventory system should be designed and why the compatible forest inventory system was significant to digital forestry in China.

  19. A rating system for determination of hazardous wastes.

    Science.gov (United States)

    Talinli, Ilhan; Yamantürk, Rana; Aydin, Egemen; Başakçilardan-Kabakçi, Sibel

    2005-11-11

    Although hazardous waste lists and their classification methodologies are nearly the same in most of the countries, there are some gaps and subjectiveness in determining the waste as hazardous waste. A rating system for the determination of waste as a hazardous waste is presented in this study which aims to overcome the problems resulted from the existing methodologies. Overall rating value (ORV) calculates and quantifies the waste as regular, non-regular or hazardous waste in an "hourglass" scale. "ORV" as a cumulative-linear formulation in proposed model consists of components such as ecological effects of the waste (Ee) in terms of four main hazard criteria: ignitability, reactivity, corrosivity and toxicity; combined potential risk (CPR) including carcinogenic effect, toxic, infectious and persistence characteristics; existing lists and their methodology (L) and decision factor (D) to separate regular and non-regular waste. Physical form (f) and quantity (Q) of the waste are considered as factors of these components. Seventeen waste samples from different sources are evaluated to demonstrate the simulation of the proposed model by using "hourglass" scale. The major benefit of the presented rating system is to ease the works of decision makers in managing the wastes.

  20. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    Science.gov (United States)

    Gajos, Katarzyna; Angelopoulou, Michailia; Petrou, Panagiota; Awsiuk, Kamil; Kakabakos, Sotirios; Haasnoot, Willem; Bernasik, Andrzej; Rysz, Jakub; Marzec, Mateusz M.; Misiakos, Konstantinos; Raptis, Ioannis; Budkowski, Andrzej

    2016-11-01

    Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays with dramatically improved both intra-chip response repeatability and assay detection sensitivity.

  1. Accuracy determination of camera system used for sport motion analysis

    Directory of Open Access Journals (Sweden)

    Bergün Meriç

    2008-10-01

    Full Text Available The aim of this study is to determine accuracy of camera system often used for motion analysis. In order to accomplish this, an industrial robot was moved with known three different trajectories and these motions were captured using three 100Hz cameras located in 3 different angles. Video data were digitized and analyzed using Simi Motion Analysis Program. With this program, angular kinematics were computed from the video data and compared with the data obtained from robot. For considering analysis of the data, average error for angle computed from average values of absolute error and root values of average of squared error is is 0.92° and 1.33°, respectively. Similarly, average error for angular velocity computed from average values of absolute error and root values of average of squared error is is 0.77° and 0.96°, respectively. These errors may result in the technique of image processing, shot speed of camera system and the limited hand sensivity of users. As motions in sports were analyzed with the camera systems, these errors must be taken in account in kinematic computation.

  2. Accuracy determination of camera system used for sport motion analysis

    Directory of Open Access Journals (Sweden)

    Bergün Meriç

    2008-10-01

    Full Text Available The aim of this study is to determine accuracy of camera system often used for motion analysis.       In order to accomplish this, an industrial robot was moved with known three different trajectories  and these motions were captured using three 100Hz cameras located in 3 different angles. Video data were digitized and analyzed using Simi Motion Analysis Program. With this program, angular kinematics were computed from the video data and compared with the data obtained from robot.       For considering analysis of the data, average error for angle computed from average values of absolute error and root values of average of squared error is is  0.92° and 1.33°, respectively. Similarly, average error for angular velocity computed from average values of absolute error and root values of average of squared error is is  0.77° and 0.96°, respectively.      These errors may result in the technique of image processing, shot speed of camera system and  the limited hand sensivity of users. As motions in sports were analyzed with the camera systems, these errors must be taken in account in kinematic computation.

  3. Scanning laser system to determine the corneal shape

    Science.gov (United States)

    Ascanio, Gabriel; Caballero-Ruiz, Alberto; Ruiz-Huerta, Leopoldo; Gonzalez-Cardel, Mario; Diaz-Uribe, Rufino

    2005-07-01

    The development and tests of a scanning system to be used to determine the corneal topography with the laser deflectometry method are presented. In this equipment, a He-Ne laser beam scans the cornea by describing a spiral trajectory generated by two components: radial and angular. The first component is produced by the displacement of a plane mirror moved by a linear pneumatic actuator. The second component is produced by passing the beam through a Dove prism which is rotating by means of a belt drive coupled to a high-speed electric motor. Tests were first performed by analyzing both components independently and then they were characterized by combining the two components. Results are discussed and compared to those of an earlier cited work.

  4. Applicability and methodology of determining sustainable yield in groundwater systems

    Science.gov (United States)

    Kalf, Frans R. P.; Woolley, Donald R.

    2005-03-01

    There is currently a need for a review of the definition and methodology of determining sustainable yield. The reasons are: (1) current definitions and concepts are ambiguous and non-physically based so cannot be used for quantitative application, (2) there is a need to eliminate varying interpretations and misinterpretations and provide a sound basis for application, (3) the notion that all groundwater systems either are or can be made to be sustainable is invalid, (4) often there are an excessive number of factors bound up in the definition that are not easily quantifiable, (5) there is often confusion between production facility optimal yield and basin sustainable yield, (6) in many semi-arid and arid environments groundwater systems cannot be sensibly developed using a sustained yield policy particularly where ecological constraints are applied. Derivation of sustainable yield using conservation of mass principles leads to expressions for basin sustainable, partial (non-sustainable) mining and total (non-sustainable) mining yields that can be readily determined using numerical modelling methods and selected on the basis of applied constraints. For some cases there has to be recognition that the groundwater resource is not renewable and its use cannot therefore be sustainable. In these cases, its destiny should be the best equitable use. producciones sostenibles en cuenca, minado parcial (no sostenible) y total (no sostenible) que pueden determinarse fácilmente utilizando métodos de modelos numéricos y seleccionados en base a restricciones aplicadas. En algunos casos tiene que reconocerse que el recurso de agua subterránea no es renovable y que por lo tanto su uso no puede ser sostenible. En estos casos su destino debe de ser el uso más equitativo.

  5. Determination of critical micelle concentration with the rotating sample system.

    Science.gov (United States)

    Kao, Linus T; Shetty, Gautam N; Gratzl, Miklós

    2008-12-01

    A novel experimental approach using the rotating sample system (RSS) is proposed here for the determination of the critical micelle concentration (CMC) of surfactants. The RSS has been conceived in our laboratory as a convection platform for physicochemical studies and analyses in microliter-sized sample drops. The scheme allows for vigorous rotation of the drop despite its small size through efficient air-liquid mechanical coupling. Thus, changes in surface properties of aqueous samples result in corresponding modulation of the hydrodynamic performance of the RSS, which can be utilized to investigate interfacial phenomena. In this work, we demonstrate that the RSS can be used to study the effects of surfactants on the surface and in the bulk of very small samples with hydrodynamic electrochemistry. Potassium ferrocyanide is employed here with cyclic voltammetry to probe the air-water interface of solutions containing Triton X-100. The CMC of this surfactant determined using this approach is 140 ppm, which agrees well with reported values obtained with conventional methods in much larger samples. The results also demonstrate that besides the CMC, variations in bulk rheological properties can also be investigated in very small specimens using the RSS with a simple method.

  6. Vision-Based Attitude and Formation Determination System Project

    Data.gov (United States)

    National Aeronautics and Space Administration — To determine pointing and position vectors in both local and inertial coordinate frames, multi-spacecraft missions typically utilize separate attitude determination...

  7. DETERMINATION OF DIFFUSION COEFFICIENTS OF BINARY LIQUID SYSTEMS

    Directory of Open Access Journals (Sweden)

    Erol İNCE

    2001-03-01

    Full Text Available The diaphragm cell method technique was used to determine the diffusion coefficients of selected binary systems (Cyclopentanol-Acetic acid, Cyclohexanol-Acetic acid and Methylcyclohexanol-Acetic acid. The technique was chosen because of simplicity and accuracy. The stirring rate was 60 rpm. The diaphragm cell was calibrated at 298.15 K by diffusing of 0.1 N KCl solution into distilled water. The experimental diaphragm cell constant (ß was found 0.09293 cm -2 . The temperature of water bath was controlled by a contact thermometer with an accuracy of ± 0.1 °C. The obtained experimental diffusion coefficients for Cyclopentanol-Acetic acid, Cyclohexanol-Acetic acid and Methylcyclohexanol - Acetic acid binary systems were 2.40 x 10 -5 cm 2 /s, 1.16 x 10 -5 cm 2 /s, 3.97 x 10 -5 cm 2 /s, respectively. Furthermore, diffusion coefficients have been estimated by the theoretical methods of Wilke - Chang and Scheibel equations and compared with the experimental results.

  8. The methane rating system to determine coal face methane conditions

    Energy Technology Data Exchange (ETDEWEB)

    Cook, A.P.; van Vuuren, J.J. [Itasca Africa (Pty) Ltd, Johannesburg (South Africa)

    2001-07-01

    Methane Rating was developed from a need in South Africa to measure coal seam gas contents, as well as emission rates into the cutting zone for mechanical miners. These are then combined and compared to the average and normal conditions to provide a risk assessment tool for continuous miner operations. The last two years have seen widespread acceptance of Methane Rating as a practical and simple means of identifying seam gas contents and emission rates during mining, and of rating the changing methane conditions. The system uses proven direct methods of methane measurement to quantify the contents and emissions, combined with an innovative rating system. Each new result is compared with the expected average or normal conditions to determine its Methane Rating between 1 and 5. The present South African national database of over 340 individual samples from 31 mines shows methane contents can normally be expected between 0,2 m{sup 3}/t and 1,4 m{sub 3}/t, with emission rates during coal cutting of 20 l/t/min to 80 l/t/min. The highest risk rated mines are presently in the Secunda and eastern Witbank areas, with the lowest risk rated mines to the west of Witbank. 6 refs., 9 figs.

  9. Tailored surface-enhanced Raman nanopillar arrays fabricated by laser-assisted replication for biomolecular detection using organic semiconductor lasers.

    Science.gov (United States)

    Liu, Xin; Lebedkin, Sergei; Besser, Heino; Pfleging, Wilhelm; Prinz, Stephan; Wissmann, Markus; Schwab, Patrick M; Nazarenko, Irina; Guttmann, Markus; Kappes, Manfred M; Lemmer, Uli

    2015-01-27

    Organic semiconductor distributed feedback (DFB) lasers are of interest as external or chip-integrated excitation sources in the visible spectral range for miniaturized Raman-on-chip biomolecular detection systems. However, the inherently limited excitation power of such lasers as well as oftentimes low analyte concentrations requires efficient Raman detection schemes. We present an approach using surface-enhanced Raman scattering (SERS) substrates, which has the potential to significantly improve the sensitivity of on-chip Raman detection systems. Instead of lithographically fabricated Au/Ag-coated periodic nanostructures on Si/SiO2 wafers, which can provide large SERS enhancements but are expensive and time-consuming to fabricate, we use low-cost and large-area SERS substrates made via laser-assisted nanoreplication. These substrates comprise gold-coated cyclic olefin copolymer (COC) nanopillar arrays, which show an estimated SERS enhancement factor of up to ∼ 10(7). The effect of the nanopillar diameter (60-260 nm) and interpillar spacing (10-190 nm) on the local electromagnetic field enhancement is studied by finite-difference-time-domain (FDTD) modeling. The favorable SERS detection capability of this setup is verified by using rhodamine 6G and adenosine as analytes and an organic semiconductor DFB laser with an emission wavelength of 631.4 nm as the external fiber-coupled excitation source.

  10. Atmospheric pressure loading effects on Global Positioning System coordinate determinations

    Science.gov (United States)

    Vandam, Tonie M.; Blewitt, Geoffrey; Heflin, Michael B.

    1994-01-01

    Earth deformation signals caused by atmospheric pressure loading are detected in vertical position estimates at Global Positioning System (GPS) stations. Surface displacements due to changes in atmospheric pressure account for up to 24% of the total variance in the GPS height estimates. The detected loading signals are larger at higher latitudes where pressure variations are greatest; the largest effect is observed at Fairbanks, Alaska (latitude 65 deg), with a signal root mean square (RMS) of 5 mm. Out of 19 continuously operating GPS sites (with a mean of 281 daily solutions per site), 18 show a positive correlation between the GPS vertical estimates and the modeled loading displacements. Accounting for loading reduces the variance of the vertical station positions on 12 of the 19 sites investigated. Removing the modeled pressure loading from GPS determinations of baseline length for baselines longer than 6000 km reduces the variance on 73 of the 117 baselines investigated. The slight increase in variance for some of the sites and baselines is consistent with expected statistical fluctuations. The results from most stations are consistent with approximately 65% of the modeled pressure load being found in the GPS vertical position measurements. Removing an annual signal from both the measured heights and the modeled load time series leaves this value unchanged. The source of the remaining discrepancy between the modeled and observed loading signal may be the result of (1) anisotropic effects in the Earth's loading response, (2) errors in GPS estimates of tropospheric delay, (3) errors in the surface pressure data, or (4) annual signals in the time series of loading and station heights. In addition, we find that using site dependent coefficients, determined by fitting local pressure to the modeled radial displacements, reduces the variance of the measured station heights as well as or better than using the global convolution sum.

  11. Determining

    Directory of Open Access Journals (Sweden)

    Bahram Andarzian

    2015-06-01

    Full Text Available Wheat production in the south of Khuzestan, Iran is constrained by heat stress for late sowing dates. For optimization of yield, sowing at the appropriate time to fit the cultivar maturity length and growing season is critical. Crop models could be used to determine optimum sowing window for a locality. The objectives of this study were to evaluate the Cropping System Model (CSM-CERES-Wheat for its ability to simulate growth, development, grain yield of wheat in the tropical regions of Iran, and to study the impact of different sowing dates on wheat performance. The genetic coefficients of cultivar Chamran were calibrated for the CSM-CERES-Wheat model and crop model performance was evaluated with experimental data. Wheat cultivar Chamran was sown on different dates, ranging from 5 November to 9 January during 5 years of field experiments that were conducted in the Khuzestan province, Iran, under full and deficit irrigation conditions. The model was run for 8 sowing dates starting on 25 October and repeated every 10 days until 5 January using long-term historical weather data from the Ahvaz, Behbehan, Dezful and Izeh locations. The seasonal analysis program of DSSAT was used to determine the optimum sowing window for different locations as well. Evaluation with the experimental data showed that performance of the model was reasonable as indicated by fairly accurate simulation of crop phenology, biomass accumulation and grain yield against measured data. The normalized RMSE were 3%, 2%, 11.8%, and 3.4% for anthesis date, maturity date, grain yield and biomass, respectively. Optimum sowing window was different among locations. It was opened and closed on 5 November and 5 December for Ahvaz; 5 November and 15 December for Behbehan and Dezful;and 1 November and 15 December for Izeh, respectively. CERES-Wheat model could be used as a tool to evaluate the effect of sowing date on wheat performance in Khuzestan conditions. Further model evaluations

  12. Challenges of Biomolecular Detection at the Nanoscale: Nanopores and Microelectrodes

    NARCIS (Netherlands)

    Mathwig, Klaus; Albrecht, Tim; Goluch, Edgar D.; Rassaei, Liza

    2015-01-01

    The interest in analytical devices, which typically rely on the reactivity of a biological component for specificity, is growing rapidly. In this Perspective, we highlight current challenges in all-electrical biosensing as these systems shrink toward the nanoscale and enable the detection of analyte

  13. Determination of Close Loop System Stability in Automobile Adaptive Cruise Control Systems

    Directory of Open Access Journals (Sweden)

    Owunna Ikechukwu

    2016-07-01

    Full Text Available The beginning of the 21st century sees auto makers pursuing research in advanced features like collision warning and avoidance system into their product. Automotive cruise control system has been undergoing development in EU since the PROMETHEUS programme in the late 1980’s, and has currently metamorphous into Adaptive Cruise Control (ACC technology which is presently emerging in the automotive market as a convenience function intended to reduce driver workload. Adaptive cruise control is the first of the new generation of advanced driver’s assistance devices to reach the market, which partially automates the driver’s task and bringing the drivers comfort into perspective. It allows the host vehicle to maintain a set speed and distance from preceding vehicles by a forward object detection sensor. The forward object detection sensor is the focal point of the ACC system, which determines and regulates vehicle acceleration and deceleration through a powertrain torque control system and an automatic brake control system. This study presents overview of adaptive cruise control system, operation principles and the advantages of integrating ACC system in automobiles. Also, the system must be stable for optimum performance, and stability of a close loop system which the cruise system is an example, was determined by calculating the controller gain (K1, K2, K3 and substituting into the characteristic equations. The stability of a close loop system for the values of K1, K2 and K3 when substituted into the characteristic equation produced a negative real part. To achieve stability in close loop systems, all the poles must have negative real values and this is in line with the values obtain for p1, p2 and p3. From the pole zero plots of 1 = (-7 ± 7.14, 2 = (-7± 11.60 and 3 = (-0.08 and -13.91, stability of the system was achieved

  14. Circular Polarization and the Origin of Biomolecular Homochirality

    Science.gov (United States)

    Bailey, Jeremy

    The origin of the homochirality of biological molecules (the fact that living systems use almost exclusively left-handed amino acids and right-handed sugars) has been a puzzle since the last century. The discovery of an excess of left-handed amino acids in the Murchison and Murray meteorites suggests that homochirality reflects a bias that existed in primordial solar-system material before the origin of life. The action of circularly polarized light is the most likely source of such an asymmetry. I will report observations of circular polarization in star formation regions which show that polarization due to dust scattering in reflection nebulae may be able account for the chiral asymmetry. Since homochirality may be a prerequisite for life, it may be that the suitability of a planet for life depends on the polarization environment in the region in which the star formed.

  15. Determining operating policies for a water resource system

    Science.gov (United States)

    Dagli, C. H.; Miles, J. F.

    1980-07-01

    The object of the study described in this paper was to find a method of determining operating policies for a set of four dams which are to be constructed on the Firat (Euphrates) River in Turkey. Each of the dams has an associated hydro-electric power plant, and there are requirements to supply water for irrigation, as well as maintaining river flows downstream of the dams into Syria and Iraq. The problem is thus complex and conventional stochastic models would entail an excessive amount of computation. Moreover, the set of feasible operating policies is so large that simulation cannot be considered a viable alternative. The method adopted might be described as adaptive planning (AP). At time l a forecast is made of the inflow values expected during the planning period and using these forecast values a deterministic model of the system is solved to obtain an operating policy for time l + 1. The forecast is updated and the model re-run at each successive time period to yield revised policies based on the latest available data. The solution obtained by this method for a five-year test period, using historical data, was within 0.4% of the optimal solution.

  16. Storage Size Determination for Grid-Connected Photovoltaic Systems

    CERN Document Server

    Ru, Yu; Martinez, Sonia

    2011-01-01

    In this paper, we study the problem of determining the size of battery storage used in grid-connected photovoltaic (PV) systems. In our setting, electricity is generated from PV and is used to supply the demand from loads. Excess electricity generated from the PV can be stored in a battery to be used later on, and electricity must be purchased from the electric grid if the PV generation and battery discharging cannot meet the demand. The objective is to minimize the electricity purchase from the electric grid while at the same time choosing an appropriate battery size. More specifically, we want to find a unique critical value (denoted as $E_{max}^c$) of the battery size such that the cost of electricity purchase remains the same if the battery size is larger than or equal to $E_{max}^c$, and the cost is strictly larger if the battery size is smaller than $E_{max}^c$. We propose an upper bound on $E_{max}^c$, and show that the upper bound is achievable for certain scenarios. For the case with ideal PV generat...

  17. Stochastic Simulation and Analysis of Biomolecular Reaction Networks

    Science.gov (United States)

    2009-01-01

    a discrete stochastic system, a hypothetical model of a generic two gene, self- assembling catalytic ligation reaction in a cell-free tran- scription...ligation reactions and the tRNA charging reactions terminate. Third, the first metabolic ligation reaction terminated when Sub_1 was depleted at about...2900 sec and subsequently, the second metabolic ligation reaction would have terminated when all of Prod_A formed by the first ligation reaction was

  18. Biomolecular Principles of Matrix Assembly Related to Fracture Resistance

    Science.gov (United States)

    2013-06-24

    mM NaHCO3 / Na2CO3 buffer. For comparison, we present RH values obtained in the same buffer/pH solutions for bovine erythrocyte carbonic...of amino acid spins systems are indicated on the plots. intrinsically disordered protein (Figure 2) that is fold-inducible and assembles to form... disordered supramolecular complexes that possess a high degree of dimensional heterogeneity (Figures 2A, 3). These protein assemblies are “plastic

  19. Anisotropy spectra for enantiomeric differentiation of biomolecular building blocks.

    Science.gov (United States)

    Evans, A C; Meinert, C; Bredehöft, J H; Giri, C; Jones, N C; Hoffmann, S V; Meierhenrich, U J

    2013-01-01

    All biopolymers are composed of homochiral building blocks, and both D-sugars and L-amino acids uniquely constitute life on Earth. These monomers were originally enantiomerically differentiated under prebiotic conditions. Particular progress has recently been made in support of the photochemical model for this differentiation: the interaction of circularly polarized light with racemic molecules is currently thought to have been the original source for life's biological homochirality. The differential asymmetric photoreactivity of particular small molecules can be characterized by both circular dichroism and anisotropy spectroscopy. Anisotropy spectroscopy, a novel derivative of circular dichroism spectroscopy, records the anisotropy factor g = Δε/ε as a function of the wavelength. Anisotropy spectroscopy promisingly affords the wavelength-dependent determination of the enantiomeric excess (ee) inducible into chiral organic molecules by photochemical irradiation with circularly polarized light. Anisotropy spectra of small molecules therefore provide unique means for characterizing the different photochemical behaviors between enantiomers upon exposure to various wavelengths of circularly polarized light. This chapter will: (1) present the theory and configuration of anisotropy spectroscopy; (2) explain experimentally recorded anisotropy spectra of selected chiral biomolecules such as amino acids; and (3) discuss the relevance of these spectra for the investigation of the origin of the molecular homochirality observed in living organisms. This review describes a new chiroptical technique that is of significance for advances in asymmetric photochemistry and that is also highly relevant for the European Space Agency Rosetta Mission, which will determine enantiomeric excesses (ees) in chiral organic molecules in cometary ices when it lands on Comet 67P/Churyumov-Gerasimenko in November 2014.

  20. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    Directory of Open Access Journals (Sweden)

    Xiliang Zheng

    2015-04-01

    Full Text Available We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity, the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  1. The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition

    Science.gov (United States)

    Zheng, Xiliang; Wang, Jin

    2015-01-01

    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

  2. Raman spectroscopy detects biomolecular changes associated with nanoencapsulated hesperetin treatment in experimental oral carcinogenesis

    Science.gov (United States)

    Gurushankar, K.; Gohulkumar, M.; Kumar, Piyush; Krishna, C. Murali; Krishnakumar, N.

    2016-03-01

    Recently it has been shown that Raman spectroscopy possesses great potential in the investigation of biomolecular changes of tumor tissues with therapeutic drug response in a non-invasive and label-free manner. The present study is designed to investigate the antitumor effect of hespertin-loaded nanoparticles (HETNPs) relative to the efficacy of native hesperetin (HET) in modifying the biomolecular changes during 7,12-dimethyl benz(a)anthracene (DMBA)-induced oral carcinogenesis using a Raman spectroscopic technique. Significant differences in the intensity and shape of the Raman spectra between the control and the experimental tissues at 1800-500 cm-1 were observed. Tumor tissues are characterized by an increase in the relative amount of proteins, nucleic acids, tryptophan and phenylalanine and a decrease in the percentage of lipids when compared to the control tissues. Further, oral administration of HET and its nanoparticulates restored the status of the lipids and significantly decreased the levels of protein and nucleic acid content. Treatment with HETNPs showed a more potent antitumor effect than treatment with native HET, which resulted in an overall reduction in the intensity of several biochemical Raman bands in DMBA-induced oral carcinogenesis being observed. Principal component and linear discriminant analysis (PC-LDA), together with leave-one-out cross validation (LOOCV) on Raman spectra yielded diagnostic sensitivities of 100%, 80%, 91.6% and 65% and specificities of 100%, 65%, 60% and 55% for classification of control versus DMBA, DMBA versus DMBA  +  HET, DMBA versus DMBA  +  HETNPs and DMBA  +  HET versus DMBA  +  HETNPs treated tissue groups, respectively. These results further demonstrate that Raman spectroscopy associated with multivariate statistical algorithms could be a valuable tool for developing a comprehensive understanding of the process of biomolecular changes, and could reveal the signatures of the

  3. Force sensors based on piezoresistive and MOSFET cantilevers for biomolecular sensing

    OpenAIRE

    Tosolini, Giordano

    2013-01-01

    Los procesos de reconocimiento biomolecular entre receptores y ligandos son muy importantes en biología. Estas biomoléculas pueden desarrollar complejos muy específicos y tener una variedad de funciones como replicación y transcripción genómica, actividad enzimática, respuesta inmune, señalamiento celular, etc. La complementariedad inequívoca mostrada por estos componentes biológicos es ampliamente utilizada para desarrollar biosensores. Dependiendo de la naturaleza de las señales que se conv...

  4. Towards a calculus of biomolecular complexes at equilibrium.

    Science.gov (United States)

    Mjolsness, Eric

    2007-07-01

    An overview is presented of the construction and use of algebraic partition functions to represent the equilibrium statistical mechanics of multimolecular complexes and their action within a larger regulatory network. Unlike many applications of equilibrium statistical mechanics, multimolecular complexes may operate with various subsets of their components present and connected to the others, the rest remaining in solution. Thus they are variable-structure systems. This aspect of their behavior may be accounted for by the use of 'fugacity' variables as a representation within the partition functions. Four principles are proposed by which the combinatorics of molecular complex construction can be reflected in the construction of their partition functions. The corresponding algebraic operations on partition functions are multiplication, addition, function composition and a less commonly used operation called contraction. Each has a natural interpretation in terms of probability distributions on multimolecular structures. Possible generalizations to nonequilibrium statistical mechanics are briefly discussed.

  5. Determinants of depression in 111 italian patients with systemic sclerosis

    Directory of Open Access Journals (Sweden)

    R. Scorza

    2011-09-01

    Full Text Available Background: A high prevalence of depressive symptoms has been described in systemic sclerosis (SSc, but no clear association with organ involvement or objective indices of disease severity has been depicted. To date, no effort has been made to determine the prevalence of depressive symptoms in Italian patients with SSc or to clarify their cause. Methods: One-hundred-eleven SSc patients were asked to fill in the Beck Depression Inventory (BDI questionnaire, the scleroderma Health Assessment Questionnaire (sHAQ and two additional questions assessing the patient’s familiar support and the social consequences of the patient’s change in physical appearnace. Results: Thirty-seven subjects (33.4% presented mild to severe depressive symptoms (BDI ³17. On univariate analysis the diffuse cutaneous form of the disease (p=0.019, higher pulmonary systolic pressures on echocardiogram (p=0.016, lower FVC percentage of predicted values (p=0.022, higher sHAQ values (p<0.001 or higher VAS values for pain (p=0.007, lung involvement (p=0.02, Raynaud’s phenomenon severity (p=0.002, ulcers severity (p=0.006 or disease severity (p<0.001, were associated with the presence of pathologic depressive symptoms. On multivariate analysis only the VAS for disease severity relevant to BDI scores (p=0.016. Social behaviour changes due to SSc-related physical involvement were reported in 14 patients (38% with depressive symptoms (p=0,006 and were more likely to be observed in younger patients (p=0.001 with a more severe Raynauds’s phenomenon (p=0.013. Conclusions: Mild to severe depressive symptoms are common in SSc patients especially in those with a worse perception of disease severity, these patients should be carefully monitored and a psychological assistance counselled whenever necessary.

  6. Virological control of groundwater quality using biomolecular tests.

    Science.gov (United States)

    Carducci, A; Casini, B; Bani, A; Rovini, E; Verani, M; Mazzoni, F; Giuntini, A

    2003-01-01

    Deep groundwater, even if generally protected, could be contaminated by surface or rain water infiltration through soil fractures, septic tanks, cesspits, land irrigation, disposal of wastewater and disposal of muds from depuration systems. The sanitary importance of such possible contamination is related to the different uses of the water and it is at the maximum level when it is intended for human use. Routine microbiological analyses do not consider viruses, only bacterial parameters, as contamination indicators. However, it is known that enteric viruses can survive a long time in deep aquifers and that they may not always be associated with bacterial indicators. The virological analysis of waters intended for drinking use is provided only as an occasional control exercised at the discretion of the sanitary authority. Technological difficulties with obtaining data about groundwater viral contamination led to a study to devise rapid and efficient methods for their detection and the application of these methods to samples from different sources. Four acid nucleic extraction techniques have been tested (classic proteinase K- phenol/chloroform, QIAamp Viral RNA Kit (Qiagen), SV Total RNA Isolation System (Promega) and NucleoSpin Virus L (Macherey-Nagel). Sensitivity and specificity of RT-PCR protocols for entero- (EV), hepatitis A (HAV) and small round structured (SRSV) viruses have been verified. Deep groundwater samples (100 L) were concentrated (2-step tangential flow ultrafiltration) and the concentrate contaminated with serial 10-fold dilutions of a known titre of poliovirus type 3. Extracted RNA was concentrated (microcon-100) and analysed by RT-PCR using specific EV primers and visualising amplification products by agarose gel electrophoresis. In addition, two different methods of RT-PCR for non-cultivable viruses have been tested: (a) RT-PCR and nested RT-PCR for HAV and (b) RT-PCR with generic primers and RT-PCR with specific primers for SRSV. Different

  7. Climate-driven population divergence in sex-determining systems

    NARCIS (Netherlands)

    Pen, Ido; Uller, Tobias; Feldmeyer, Barbara; Harts, Anna; While, Geoffrey M.; Wapstra, Erik

    2010-01-01

    Sex determination is a fundamental biological process, yet its mechanisms are remarkably diverse(1,2). In vertebrates, sex can be determined by inherited genetic factors or by the temperature experienced during embryonic development(2,3). However, the evolutionary causes of this diversity remain unk

  8. Transitions between sex-determining systems in reptiles and amphibians.

    Science.gov (United States)

    Sarre, Stephen D; Ezaz, Tariq; Georges, Arthur

    2011-01-01

    Important technological advances in genomics are driving a new understanding of the evolution of sex determination in vertebrates. In particular, comparative chromosome mapping in reptiles has shown an intriguing distribution of homology in sex chromosomes across reptile groups. When this new understanding is combined with the widespread distribution of genetic and temperature-dependent sex-determination mechanisms among reptiles, it is apparent that transitions between modes have occurred many times, as they have for amphibians (particularly between male and female heterogamety). It is also likely that thermosensitivity in sex determination is a key factor in those transitions in reptiles, and possibly in amphibians too. New models of sex determination involving temperature thresholds are providing the framework for the investigation of transitions and making possible key predictions about the homologies and sex-determination patterns expected among taxa in these groups. Molecular cytogenetics and other genomic approaches are essential to providing the fundamental material necessary to make advances in this field.

  9. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    Energy Technology Data Exchange (ETDEWEB)

    Gajos, Katarzyna, E-mail: kasia.fornal@uj.edu.pl [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Angelopoulou, Michailia; Petrou, Panagiota [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Awsiuk, Kamil [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Kakabakos, Sotirios [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Haasnoot, Willem [RIKILT Wageningen UR, Akkermaalsbos 2, 6708 WB Wageningen (Netherlands); Bernasik, Andrzej [Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Rysz, Jakub [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Marzec, Mateusz M. [Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Misiakos, Konstantinos; Raptis, Ioannis [Department of Microelectronics, Institute of Nanoscience and Nanotechnology, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Budkowski, Andrzej [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland)

    2016-11-01

    Highlights: • Optimization of probe immobilization with robotic spotter printing overlapping spots. • In-situ inspection of microstructured surfaces of biosensors integrated on silicon. • Imaging and chemical analysis of immobilization, surface blocking and immunoreaction. • Insight with molecular discrimination into step-by-step sensor surface modifications. • Optimized biofunctionalization improves sensor sensitivity and response repeatability. - Abstract: Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays

  10. A new approach to implement absorbing boundary condition in biomolecular electrostatics.

    Science.gov (United States)

    Goni, Md Osman

    2013-01-01

    This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.

  11. DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith

    2014-01-01

    Full Text Available We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc., a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

  12. Characterization of a nanoscale S-layer protein based template for biomolecular patterning.

    Science.gov (United States)

    Wong, Wing Sze; Yung, Pun To

    2014-01-01

    Well organized template for biomolecular conjugation is the foundation for biosensing. Most of the current devices are fabricated using lithographic patterning processes and self-assembly monolayer (SAM) methods. However, the research toward developing a sub-10 nm patterned, self-regenerated template on various types of substrates is limited, mainly due to the limited functional groups of the building material. Bacterial surface layer proteins (S-layer proteins) can self-assemble into ordered lattice with regular pore sizes of 2-8 nm on different material supports and interfaces. The ordered structure can regenerate after extreme variations of solvent conditions. In this work, we developed a nanoscale biomolecular template based on S-layer proteins on gold surface for fabrication of sensing layer in biosensors. S-layer proteins were isolated from Bacillus cereus, Lysinibacillus sphaericus and Geobacillus stearothermophilus. Protein concentrations were measured by Bradford assay. The protein purities were verified by SDS-PAGE, showing molecular weights ranging from 97-135 kDa. The hydrophilicity of the substrate surface was measured after surface treatments of protein recrystallization. Atomic force microscopic (AFM) measurement was performed on substrate surface, indicating a successful immobilization of a monolayer of S-layer protein with 8-9 nm height on gold surface. The template can be applied on various material supports and acts as a self-regenerated sensing layer of biosensors in the future.

  13. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics.

    Science.gov (United States)

    Kubelka, Jan

    2009-04-01

    Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes.

  14. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

    Science.gov (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2.

  15. Submicrometer Hall sensors for detection of magnetic nanoparticles in biomolecular sensing

    Science.gov (United States)

    Mihajlovic, Goran; Xiong, P.; von Molnar, S.; Ohtani, K.; Ohno, H.; Field, M.; Sullivan, G. J.

    2006-03-01

    Significant progress has been made in the recent years in synthesis and biomolecular functionalization of magnetic nanoparticles. These magnetic bio-nanolabels can be utilized as protein or gene markers in biomolecular sensing assays, in contrast to the much larger micron sized magnetic beads that are usually limited to cell labeling. However, the low magnetic moments of individual nanoparticles (10^4-10^5 μB) render their sensitive detection still a challenging task. In order to address this issue we are developing miniaturized Hall sensors from InAs/AlSb quantum well semiconductor heterostructures with active Hall cross areas down to 300 nm x 300 nm. Our preliminary characterization measurements performed at room temperature show functional devices with magnetic field resolution < 100 μT/√Hz at frequencies above 100 Hz, yielding a moment sensitivity ˜ 10^5 μB. In addition to the progress in improving the moment sensitivity of the submicrometer Hall detectors, we will also present efforts in device integration with on-chip microcoils for the generation of local magnetic excitation fields. Results on nanoparticle detection will also be presented.

  16. Gas-chromatographic determination of aluminum in catalytic systems

    Energy Technology Data Exchange (ETDEWEB)

    Astapova, T.I.; Kutepova, A.I.; Frolova, O.D.

    1987-11-10

    The authors studied conditions for the chromatographic determination of aluminum in the form of a complex with pentane-2,4-dione in pilot plant-produced samples of GIAP-16, GIAP-16-2, SPM catalysts, talums and kaolins, aluminum oxides, and hydroxides. The influence of Zn, Mg, Ca, Na, Ni, Ti, and Mn on the extraction and the chromatographic determination of aluminum was studied.

  17. Studying chemical reactions in biological systems with MBN Explorer

    DEFF Research Database (Denmark)

    Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.

    2016-01-01

    The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies....... for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems....

  18. Determinants of system transparency and its influence on trust in and reliance on unmanned robotic systems

    Science.gov (United States)

    Ososky, Scott; Sanders, Tracy; Jentsch, Florian; Hancock, Peter; Chen, Jessie Y. C.

    2014-06-01

    Increasingly autonomous robotic systems are expected to play a vital role in aiding humans in complex and dangerous environments. It is unlikely, however, that such systems will be able to consistently operate with perfect reliability. Even less than 100% reliable systems can provide a significant benefit to humans, but this benefit will depend on a human operator's ability to understand a robot's behaviors and states. The notion of system transparency is examined as a vital aspect of robotic design, for maintaining humans' trust in and reliance on increasingly automated platforms. System transparency is described as the degree to which a system's action, or the intention of an action, is apparent to human operators and/or observers. While the physical designs of robotic systems have been demonstrated to greatly influence humans' impressions of robots, determinants of transparency between humans and robots are not solely robot-centric. Our approach considers transparency as emergent property of the human-robot system. In this paper, we present insights from our interdisciplinary efforts to improve the transparency of teams made up of humans and unmanned robots. These near-futuristic teams are those in which robot agents will autonomously collaborate with humans to achieve task goals. This paper demonstrates how factors such as human-robot communication and human mental models regarding robots impact a human's ability to recognize the actions or states of an automated system. Furthermore, we will discuss the implications of system transparency on other critical HRI factors such as situation awareness, operator workload, and perceptions of trust.

  19. Determinants of educational systems of Bophuthatswana and Botswana / Jacob Herman Kgosi Malao

    OpenAIRE

    Malao, Jacob Herman Kgosi

    1985-01-01

    In the opening chapter the following matters are looked into: * PROBLEM OF RESEARCH The problem of research is: - to determine whether the influences of the Republic of South Africa on the Bophuthatswana system of education and that of England on Botswana are responsible for differences of the educational systems of Bophuthatswana and Botswana; - to determine whether there are other determinants of the systems in question; and - a comparison of the determinants of the education...

  20. Functional Systems and Culturally-Determined Cognitive Differences.

    Science.gov (United States)

    Wiseman, Richard L.

    Noting that one means of better understanding the nature of cultural differences is to elucidate the cognitive differences between members of differing cultures, this paper examines Alexander Luria's sociohistorical theory of functional cognitive systems. The paper first describes Luria's notion of functional systems, the crux of which postulates…

  1. Strategies for high-precision Global Positioning System orbit determination

    Science.gov (United States)

    Lichten, Stephen M.; Border, James S.

    1987-01-01

    Various strategies for the high-precision orbit determination of the GPS satellites are explored using data from the 1985 GPS field test. Several refinements to the orbit determination strategies were found to be crucial for achieving high levels of repeatability and accuracy. These include the fine tuning of the GPS solar radiation coefficients and the ground station zenith tropospheric delays. Multiday arcs of 3-6 days provided better orbits and baselines than the 8-hr arcs from single-day passes. Highest-quality orbits and baselines were obtained with combined carrier phase and pseudorange solutions.

  2. Investigation of the Human Disease Osteogenesis Imperfecta: A Research-Based Introduction to Concepts and Skills in Biomolecular Analysis

    Science.gov (United States)

    Mate, Karen; Sim, Alistair; Weidenhofer, Judith; Milward, Liz; Scott, Judith

    2013-01-01

    A blended approach encompassing problem-based learning (PBL) and structured inquiry was used in this laboratory exercise based on the congenital disease Osteogenesis imperfecta (OI), to introduce commonly used techniques in biomolecular analysis within a clinical context. During a series of PBL sessions students were presented with several…

  3. Biochemical and biomolecular aspects of oxidative stress due to acute and severe hypoxia in human muscle tissue.

    Science.gov (United States)

    Corbucci, G G; Sessego, R; Velluti, C; Salvi, M

    1995-01-01

    Mitochondrial oxidative stress was investigated in severe and acute hypoxia and in reperfusion applied to human muscle tissues. The biochemical and biomolecular relationship between the response of the respiratory-chain enzymic complexes and the metabolism of specific hypoxia stress proteins (HSP) suggest an adaptive mechanism which antagonizes the oxidative damage due to acute and severe tissue hypoxia.

  4. A Virtual Instrument System for Determining Sugar Degree of Honey.

    Science.gov (United States)

    Wu, Qijun; Gong, Xun

    2015-01-01

    This study established a LabVIEW-based virtual instrument system to measure optical activity through the communication of conventional optical instrument with computer via RS232 port. This system realized the functions for automatic acquisition, real-time display, data processing, results playback, and so forth. Therefore, it improved accuracy of the measurement results by avoiding the artificial operation, cumbersome data processing, and the artificial error in optical activity measurement. The system was applied to the analysis of the batch inspection on the sugar degree of honey. The results obtained were satisfying. Moreover, it showed advantages such as friendly man-machine dialogue, simple operation, and easily expanded functions.

  5. A Virtual Instrument System for Determining Sugar Degree of Honey

    Directory of Open Access Journals (Sweden)

    Qijun Wu

    2015-01-01

    Full Text Available This study established a LabVIEW-based virtual instrument system to measure optical activity through the communication of conventional optical instrument with computer via RS232 port. This system realized the functions for automatic acquisition, real-time display, data processing, results playback, and so forth. Therefore, it improved accuracy of the measurement results by avoiding the artificial operation, cumbersome data processing, and the artificial error in optical activity measurement. The system was applied to the analysis of the batch inspection on the sugar degree of honey. The results obtained were satisfying. Moreover, it showed advantages such as friendly man-machine dialogue, simple operation, and easily expanded functions.

  6. System for controllable magnetic measurement with direct field determination

    Science.gov (United States)

    Stupakov, O.

    2012-02-01

    This work describes a specially designed setup for magnetic hysteresis and Barkhausen noise measurements. The setup combines two main elements: an improved fast algorithm to control the waveform of magnetic induction and simultaneous direct determination of the magnetic field. The digital feedback algorithm uses only the previous measurement cycle to correct the magnetization voltage without any additional correlation parameter; it usually converges after several tens of cycles. The magnetic field is measured at the sample surface using a vertically mounted array of sensitive Hall sensors. Linear extrapolation of the tangential field profile to the sample surface determines the true waveform of the magnetic field. This unique combination of physically based control for both parameters of the magnetization process provides stable and reliable results, which are independent of a specified experimental configuration. This is illustrated for the industrially attractive measurements of non-oriented electrical steels with a 50 Hz sinusoidal induction waveform.

  7. GRAIL Science Data System Orbit Determination : Approach, Strategy, and Performance

    Science.gov (United States)

    Fahnestock, Eugene; Asmar, Sami; Park, Ryan; Strekalov, Dmitry; Yuan, Dah-Ning; Harvey, Nate; Kahan, Daniel; Konopliv, Alex; Kruizinga, Gerhard; Oudrhiri, Kamal; Paik, Meegyeong

    2013-01-01

    This paper details orbit determination techniques and strategies employed within each stage of the larger iterative process of preprocessing raw GRAIL data into the gravity science measurements used within gravity field solutions. Each orbit determination pass used different data, corrections to them, and/or estimation parameters. We compare performance metrics among these passes. For example, for the primary mission, the magnitude of residuals using our orbits progressed from approximately or equal to19.4 to 0.077 approximately or equal to m/s for inter-satellite range rate data and from approximately or equal to 0.4 to approximately or equal to 0.1 mm/s for Doppler data.

  8. Experimentally determined chaotic phase synchronization in a neuronal system

    Science.gov (United States)

    Makarenko, Vladimir; Llinás, Rodolfo

    1998-01-01

    Mathematical analysis of the subthreshold oscillatory properties of inferior olivary neurons in vitro indicates that the oscillation is nonlinear and supports low dimensional chaotic dynamics. This property leads to the generation of complex functional states that can be attained rapidly via phase coherence that conform to the category of “generalized synchronization.” Functionally, this translates into neuronal ensemble properties that can support maximum functional permissiveness and that rapidly can transform into robustly determined multicellular coherence. PMID:9861041

  9. CORPORATE GOVERNANCE – DETERMINANT OF MOLDOVAN BANKING SYSTEM STABILITY

    Directory of Open Access Journals (Sweden)

    Dorina CLICHICI

    2015-04-01

    Full Text Available Recent events recorded in the banking sector of the Republic of Moldova – establishing special administration in three commercial banks by the National Bank of Moldova (NBM – have highlighted the significant role which the quality of corporate governance presents for banking system. The aim of this paper is to identify the challenges of corporate governance for the stability of the Moldovan banking system and destabilizing effects of weak corporate governance structures within banking institutions and analyze the consequences of corporate governance deficiencies. For achieving the goal the author conducted a detailed analysis of normative acts regulating the banking system in order to identify the existing gaps regarding this subject and analyzed recent performances of commercial banks in Moldova. Despite some progress in addressing the recommendations of the International Monetary Fund (IMF and the satisfactory reported performance of banks, there are serious governance problems in several banks including the largest ones.

  10. Quality determination of Mozafati dates using Mamdani fuzzy inference system

    Directory of Open Access Journals (Sweden)

    N. Alavi

    2013-06-01

    Full Text Available The date fruit, which is produced mostly in the hot arid regions of Southern Asia and North Africa, in large quantities, is marketed all over the world as an important crop. Date grading is an important process for producers and affects the fruit quality evaluation and export market. In this research Mamdani fuzzy inference system (MFIS was applied as a decision making technique to classify the Mozafati dates based on quality. Two date parameters including the length and freshness were measured for 500 date fruits. These dates were graded by both a human expert and MFIS. Grading results obtained from fuzzy system showed 91% general conformity with the experimental results.

  11. Determination of selectivity of HPLC systems by correspondence factor analysis

    Institute of Scientific and Technical Information of China (English)

    Yuan Wang; Jun Yang; Xin Lu; Guo Wang Xu

    2007-01-01

    Correspondence factor analysis (CFA) was employed to study the selectivity of 14 HPLC systems, The tested LC systems were classified as reversed-phase (RP), ion-exchange (IE) and hydrophilic interaction chromatography (HILIC) modes. It was found that the retentions of the hydrophilic solutes on HILIC column were significantly influenced by the second-order effects besides their hydrophilic properties. Organic modifiers and residue silanol groups on silica surface both participated in retention. HypersilTM amino column performed separation in the HILIC mode at appropriate conditions, and its retention mechanism was more similar to that of HILIC silica column than that of HILIC column coating poly(aspartamide) groups.

  12. Determinants of quality management systems implementation in hospitals

    NARCIS (Netherlands)

    Wardhani, Viera; Utarini, Adi; van Dijk, Jitse Pieter; Post, Doeke; Groothoff, Johan Willem

    2009-01-01

    Objective: To identify the problems and facilitating factors in the implementation of quality management system (QMS) in hospitals through a systematic review. Method: A search strategy was pet-formed on the Medline database for articles written in English published between 1992 and early 2006. Usin

  13. Classical system boundaries cannot be determined within quantum Darwinism

    Science.gov (United States)

    Fields, Chris

    Multiple observers who interact with environmental encodings of the states of a macroscopic quantum system S as required by quantum Darwinism cannot demonstrate that they are jointly observing S without a joint a priori assumption of a classical boundary separating S from its environment E. Quantum Darwinism cannot, therefore, be regarded as providing a purely quantum-mechanical explanation of the "emergence" of classicality.

  14. An ultrasonic system for determining papaya physiological properties

    Science.gov (United States)

    Ibrahim, Sallehuddin; Ramli, Azlin; Yunus, Mohd Amri Md

    2015-05-01

    There is an increasing need for high quality fruit. As such it is important to have a fast, accurate and reliable method for measuring and monitoring the quality of fruit from the field to the consumer. This paper presents an investigation on the use of a non-destructive ultrasonic system which can be used to measure the quality of papaya.

  15. Determining the quality evaluation procedures using the expert systems

    CERN Document Server

    Holban, N; Iancu, E

    2010-01-01

    At this time, quality is a strategic instrument of the entities' global management, but it is also a determining element of their competitive spirit. The importance given to quality is abundantly found in the preoccupations of the European Union's Minister Board, by elaborating documents with a high impact over the quality of products/ services in special, and organizations in general. We live in an era, when the evolution of the social life puts the accent more and more on quality, resulted from various processes, at the level of various domains of the economical and social development.

  16. An Autonomous Orbit Determination System for Earth Satellites

    Science.gov (United States)

    1989-12-01

    these points is warranted. For example, low-Earth orbits ( LEO ) can be expected to approach e - 0 with time, so it is particularly useful to examine how...0.77887 e + 0.52875 e x y z 7 Canis Major A A A Cairs) M-0.18485 e + 0.93984 e - 0.28728 e (Sirus) -xyz A A A 8 a Leo -0.86275 e + 0.46061 e...Filters for Orbit Determination and Estimation, PhD Dissertation. University of Illinois, Urbana-Champaign IL, 1986 (AD-A170680). 12. Brouwer , Dirk

  17. Determination and discussion hydraulic retention time in membrane bioreactor system

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Based on the microorganism kinetic model, the formulafor computing hydraulic retention time in a membrane bioreactorsystem (MBR) is derived. With considering HRT as an evaluationindex a combinational approach was used to discuss factors whichhave an effect on MBR. As a result, the influencing factors werelisted in order from strength to weakness as: maximum specificremoval rate K, saturation constant Ks, maintenance coefficient m,Moreover, the formula was simplified, whose parameters wereexperimentally determined in petrochemical wastewater treatment. The simplified formula is (=1.1((1/(-1)(Ks+S)/KX0, forpetrochemical wastewater treatment K and Ks equaled 0.185 and154.2, respectively.

  18. 48 CFR 19.303 - Determining North American Industry Classification System (NAICS) codes and size standards.

    Science.gov (United States)

    2010-10-01

    ... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false Determining North American Industry Classification System (NAICS) codes and size standards. 19.303 Section 19.303 Federal Acquisition... Classification System (NAICS) codes and size standards. (a) The contracting officer shall determine...

  19. Self-chemisorption of azurin on functionalized oxide surfaces for the implementation of biomolecular devices

    Energy Technology Data Exchange (ETDEWEB)

    Biasco, A.; Maruccio, G.; Visconti, P.; Bramanti, A.; Calogiuri, P.; Cingolani, R.; Rinaldi, R

    2004-06-01

    In this work, we investigate the formation of redox protein Azurin (Az) monolayers on functionalized oxygen exposing surfaces. These metallo-proteins mediate electron transfer in the denitrifying chain of Pseudomonas bacteria and exhibit self-assembly properties, therefore they are good candidates for bio-electronic applications. Azurin monolayers are self-assembled onto silane functionalized surfaces and characterized by atomic force microscopy (AFM). We show also that a biomolecular field effect transistor (FET) in the solid state can be implemented by interconnecting an Azurin monolayer immobilized on SiO{sub 2} with two gold nanoelectrodes. Transport experiments, carried out at room temperature and ambient pressure, show FET behavior with conduction modulated by the gate potential.

  20. In situ characterization of nanoparticle biomolecular interactions in complex biological media by flow cytometry

    Science.gov (United States)

    Lo Giudice, Maria Cristina; Herda, Luciana M.; Polo, Ester; Dawson, Kenneth A.

    2016-11-01

    Nanoparticles interacting with, or derived from, living organisms are almost invariably coated in a variety of biomolecules presented in complex biological milieu, which produce a bio-interface or `biomolecular corona' conferring a biological identity to the particle. Biomolecules at the surface of the nanoparticle-biomolecule complex present molecular fragments that may be recognized by receptors of cells or biological barriers, potentially engaging with different biological pathways. Here we demonstrate that using intense fluorescent reporter binders, in this case antibodies bound to quantum dots, we can map out the availability of such recognition fragments, allowing for a rapid and meaningful biological characterization. The application in microfluidic flow, in small detection volumes, with appropriate thresholding of the detection allows the study of even complex nanoparticles in realistic biological milieu, with the emerging prospect of making direct connection to conditions of cell level and in vivo experiments.

  1. A Review of Salam Phase Transition in Protein Amino Acids Implication for Biomolecular Homochirality

    CERN Document Server

    Bai, F; Bai, Fan; Wang, Wenqing

    2002-01-01

    The origin of chirality, closely related to the evolution of life on the earth, has long been debated. In 1991, Abdus Salam suggested a novel approach to achieve biomolecular homochirality by a phase transition. In his subsequent publication, he predicted that this phase transition could eventually change D-amino acids to L-amino acids as C -H bond would break and H atom became a superconductive atom. Since many experiments denied the configuration change in amino acids, Salam hypothesis aroused suspicion. This paper is aimed to provide direct experimental evidence of a phase transition in alanine, valine single crystals but deny the configuration change of D- to L- enantiomers. New views on Salam phase transition are presented to revalidate its great importance in the origin of homochirality.

  2. Effect of temperature and magnetic field on the photocurrent response of biomolecular bulk-hetero junction

    Science.gov (United States)

    Tajima, Hiroyuki; Sekiguchi, Yusuke; Matsuda, Masaki

    2012-02-01

    The photocurrent responses were investigated for the biomolecular bulk-hetero junction of chlorophyll α (Chl-α) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-1-phenyl-(6,6)C61 (PCBM) in the temperature range between 300 K and 1.5 K under the magnetic field up to 8 T. The chopped-light photocurrent decreases on lowering the temperature. Below 10 K, photocurrent decrease was observed under the applied magnetic field. Decay of the photocurrent observed at 10 K was ascribed to the formation of the charged trap under light irradiation. The magnetic field effect (MFE) observed in this device was found to be very similar to that observed in P3HT:PCBM bulk-hetero junction at low temperatures.

  3. Gold nanoshells with gain-assisted silica core for ultra-sensitive bio-molecular sensors

    Science.gov (United States)

    Tao, Yifei; Guo, Zhongyi; Zhang, Anjun; Zhang, Jingran; Wang, Benyang; Qu, Shiliang

    2015-08-01

    A novel bio-molecular nanostructured sensor composed of Au spherical nanoshell and gain-assisted silica-core has been proposed and investigated theoretically, which shows a superior performance compared to the existing structured sensor. Using quasi-static approximation calculation, it is found that the scattering efficiency and the quality factor of SPR can be enhanced greatly by introducing proper amount of gain. The simulated results demonstrate that our designed Au spherical nanoshell and gain-assisted silica-core can obtain as high as 166.7 nm/RIU for the sensitivity of refractive index, and the sensors' figure of merit is enhanced 2000 times nearly compared to that of g=0, which indicates that the designed spherical core-shell sensors have the powerful ability to detect a subtle change in the concentration of its background medium.

  4. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.

    2011-11-07

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  5. Model for determining and optimizing delivery performance in industrial systems

    Directory of Open Access Journals (Sweden)

    Fechete Flavia

    2017-01-01

    Full Text Available Performance means achieving organizational objectives regardless of their nature and variety, and even overcoming them. Improving performance is one of the major goals of any company. Achieving the global performance means not only obtaining the economic performance, it is a must to take into account other functions like: function of quality, delivery, costs and even the employees satisfaction. This paper aims to improve the delivery performance of an industrial system due to their very low results. The delivery performance took into account all categories of performance indicators, such as on time delivery, backlog efficiency or transport efficiency. The research was focused on optimizing the delivery performance of the industrial system, using linear programming. Modeling the delivery function using linear programming led to obtaining precise quantities to be produced and delivered each month by the industrial system in order to minimize their transport cost, satisfying their customers orders and to control their stock. The optimization led to a substantial improvement in all four performance indicators that concern deliveries.

  6. System and method for determining velocity of electrically conductive fluid

    Science.gov (United States)

    Polzin, Kurt A. (Inventor); Korman, Valentin (Inventor); Markusic, Thomas E. (Inventor); Stanojev, Boris Johann (Inventor)

    2008-01-01

    A flowing electrically-conductive fluid is controlled between an upstream and downstream location thereof to insure that a convection timescale of the flowing fluid is less than a thermal diffusion timescale of the flowing fluid. First and second nodes of a current-carrying circuit are coupled to the fluid at the upstream location. A current pulse is applied to the current-carrying circuit so that the current pulse travels through the flowing fluid to thereby generate a thermal feature therein at the upstream location. The thermal feature is convected to the downstream location where it is monitored to detect a peak associated with the thermal feature so-convected. The velocity of the fluid flow is determined using a time-of-flight analysis.

  7. Refractive Index Compensation in Over-Determined Interferometric Systems

    Directory of Open Access Journals (Sweden)

    Zdeněk Buchta

    2012-10-01

    Full Text Available We present an interferometric technique based on a differential interferometry setup for measurement under atmospheric conditions. The key limiting factor in any interferometric dimensional measurement are fluctuations of the refractive index of air representing a dominating source of uncertainty when evaluated indirectly from the physical parameters of the atmosphere. Our proposal is based on the concept of an over-determined interferometric setup where a reference length is derived from a mechanical frame made from a material with a very low thermal coefficient. The technique allows one to track the variations of the refractive index of air on-line directly in the line of the measuring beam and to compensate for the fluctuations. The optical setup consists of three interferometers sharing the same beam path where two measure differentially the displacement while the third evaluates the changes in the measuring range, acting as a tracking refractometer. The principle is demonstrated in an experimental setup.

  8. Neural Network Enhanced Structure Determination of Osteoporosis, Immune System, and Radiation Repair Proteins Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation will utilize self learning neural network technology to determine the structure of osteoporosis, immune system disease, and excess radiation...

  9. [Mobile health and health systems: determining progress in global health].

    Science.gov (United States)

    Frenk, Julio

    2015-01-01

    Usually when we talk about information technologies we are speaking about the technology itself and its contents. In this article I want to focus on mobile technologies for health (mobile health), but not so much on the content of mobile health but in its context, represented by the health systems where these technologies are deployed. The central message is that in order to capitalize on the potential of the mobile communications revolution, it is not only necessary to innovate in the field of the same technologies but also in the institutions that enable these technologies to reach their potential beneficiaries.

  10. Determining intrafractional prostate motion using four dimensional ultrasound system

    DEFF Research Database (Denmark)

    Baker, Mariwan; Behrens, Claus F.

    2016-01-01

    ) the prostate was monitored for 2 to 2.5 min, a typical beam-on time to deliver a RapidArc® radiotherapy fraction. The patients were instructed to remain motionless in supine position throughout the US scans. They were also requested to comply with a bladder-filling protocol. In total, 51 monitoring curves were....... Methods: Ten prostate patients were ultrasound (US) scanned at the time of CT imaging and once a week during their course of radiotherapy treatment in an ethics-approved study, using the transperineal Clarity autoscan system (Clarity®, Elekta Inc., Stockholm, Sweden). At each US scanning session (fraction...

  11. Determining the contribution of the energy systems during exercise.

    Science.gov (United States)

    Artioli, Guilherme G; Bertuzzi, Rômulo C; Roschel, Hamilton; Mendes, Sandro H; Lancha, Antonio H; Franchini, Emerson

    2012-03-20

    One of the most important aspects of the metabolic demand is the relative contribution of the energy systems to the total energy required for a given physical activity. Although some sports are relatively easy to be reproduced in a laboratory (e.g., running and cycling), a number of sports are much more difficult to be reproduced and studied in controlled situations. This method presents how to assess the differential contribution of the energy systems in sports that are difficult to mimic in controlled laboratory conditions. The concepts shown here can be adapted to virtually any sport. The following physiologic variables will be needed: rest oxygen consumption, exercise oxygen consumption, post-exercise oxygen consumption, rest plasma lactate concentration and post-exercise plasma peak lactate. To calculate the contribution of the aerobic metabolism, you will need the oxygen consumption at rest and during the exercise. By using the trapezoidal method, calculate the area under the curve of oxygen consumption during exercise, subtracting the area corresponding to the rest oxygen consumption. To calculate the contribution of the alactic anaerobic metabolism, the post-exercise oxygen consumption curve has to be adjusted to a mono or a bi-exponential model (chosen by the one that best fits). Then, use the terms of the fitted equation to calculate anaerobic alactic metabolism, as follows: ATP-CP metabolism = A(1;) (mL . s(-1)) x t(1;) (s). Finally, to calculate the contribution of the lactic anaerobic system, multiply peak plasma lactate by 3 and by the athlete's body mass (the result in mL is then converted to L and into kJ). The method can be used for both continuous and intermittent exercise. This is a very interesting approach as it can be adapted to exercises and sports that are difficult to be mimicked in controlled environments. Also, this is the only available method capable of distinguishing the contribution of three different energy systems. Thus, the method

  12. Some Limitations of BIOLOG System for Determining Soil Microbial Community

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A laboratory experiment was conducted to evaluate the effect of triphenyltetrazolium chloride (TTC)on soil microorganisms and the availability of pH characterization medium in BIOLOG plates. Applicationof TTC decreased the color development sharply and resulted in a great biocidal effect on the growth andreproduction of soil microorganisms, indicating that TTC can affect the discrimination on soil microbialcommunity. The microtitration plates with 21 carbon sources and two different pH levels (4.7 and 7.0) wereused to determine microbial community structure of eight red soils. The average utilization (average wellcolour development) of the carbon sources in the plates with different pH levels generally followed the samesigmoidal pattern as that in the traditional BIOLOG plates, but the pH 4.7 plates increased the discrimination of this technique, compared with the pH 7.0 plates. Since most tested soils are acid, it seemed that it's better to use a suitable pH characterization medium for a specific soil in the sole carbon source test.

  13. Gravity Probe B Timing System and Roll Phase Determination

    Science.gov (United States)

    Jie, Li; Kolodziejczak, Jeffery

    2007-01-01

    An oven-controlled crystal oscillator at 16.368 MHz provides clock signals to all GP-B components and synchronizes the data collection, transmission and processing. The sampled science data signals are stamped with the vehicle time, a counter of the 10Hz data strobe divided down from the clock. The GPS receiver supplies an external reference for time transfer between the vehicle time and coordinated universal time. Ground and space flight tests show the time transfer error is within 1 microsecond. The time latency between the effective sample time of science signals and the stamped vehicle time is verified to 1 ms in the ground tests. The GP-B satellite is controlled to roll with a period of 77.5 sec about an axis along the direction to the guide star to average out the disturbance torques fixed to the body of the satellite and reduce the gyroscope readout noise. The roll phase is determined on the ground to high accuracy with the telemetry data from two star trackers and used in the data analysis to separate the drifts of gyroscope spin axes in the orbital plane and perpendicular to the orbital plane. The flight data shows that the roll phase is controlled to within 40 arcsec with a measurement uncertainty of 7 arcsec.

  14. Determination of fish trophic levels in an estuarine system

    Science.gov (United States)

    Pasquaud, S.; Pillet, M.; David, V.; Sautour, B.; Elie, P.

    2010-01-01

    The concept of trophic level is particularly relevant in order to improve knowledge of the structure and the functioning of an ecosystem. A precise estimation of fish trophic levels based on nitrogen isotopic signatures in environments as complex and fluctuant as estuaries requires a good description of the pelagic and benthic trophic chains and a knowledge of organic matter sources at the bottom. In this study these points are considered in the case of the Gironde estuary (south west France, Europe). To obtain a good picture of the food web, fish stomach content analyses and a bibliographic synthesis of the prey feeding ecology were carried out. Fish trophic levels were calculated from these results and δ 15N data. The feeding link investigation enabled us to identify qualitatively and quantitatively the different preys consumed by each fish group studied, to distinguish the prey feeding on benthos from those feeding on pelagos and to characterize the different nutritive pools at the base of the system. Among the species studied, only Liza ramada and the flatfish ( Platichthys flesus and Solea solea) depend mainly on benthic trophic compartments. All the other fish groups depend on several trophic (benthic and/or pelagic) sources. These results enabled us to correct the calculation of fish trophic levels which are coherent with their feeding ecology data obtained from the nitrogen isotopic integrative period. The present work shows that trophic positions are linked with the feeding ecology of fish species and vary according to individual size. Ecological data also allow the correction of the isotopic data by eliminating absurd results and showing the complementarity of the two methods. This work is the first to consider source variability in the fish food web. This is an indispensable step for trophic studies in a dynamic environment. The investigation of matter fluxes and recycling processes at the food web base would provide a useful improvement in future

  15. Bacterial imbalance of the vaginal flora: a cytological and biomolecular concept of Gardnerella vaginalis

    NARCIS (Netherlands)

    Klomp, J.M.

    2008-01-01

    Since 1996 all women aged 30 to 60 years are invited for a cervical smear on a 5 year interval. KOPAC, the Dutch national coding system for cervical smears, introduced for determination of cervical abnormalities also evaluates the inflammatory status of the vaginal flora. In this system dysbacterios

  16. UNIQUAC interaction parameters for alkane/amine systems determined by Molecular Mechanics

    DEFF Research Database (Denmark)

    Jonsdottir, Svava Osk; Klein, R. A.; Rasmussen, Kjeld

    1996-01-01

    UNIQUAC interaction parameters have been successfully determined for three alkane/primary amine systems using a Molecular Mechanics method called the Consistent Force Field. Interaction parameters for alkane/alkane and alkane/ketone systems had been determined previously using this method...

  17. Tibialis anterior muscle needle biopsy and sensitive biomolecular methods: a useful tool in myotonic dystrophy type 1

    Directory of Open Access Journals (Sweden)

    S. Iachettini

    2015-10-01

    Full Text Available Myotonic dystrophy type 1 (DM1 is a neuromuscular disorder caused by a CTG repeat expansion in 3’UTR of DMPK gene. This mutation causes accumulation of toxic RNA in nuclear foci leading to splicing misregulation of specific genes. In view of future clinical trials with antisense oligonucleotides in DM1 patients, it is important to set up sensitive and minimally-invasive tools to monitor the efficacy of treatments on skeletal muscle. A tibialis anterior (TA muscle sample of about 60 mg was obtained from 5 DM1 patients and 5 healthy subjects through a needle biopsy. A fragment of about 40 mg was used for histological examination and a fragment of about 20 mg was used for biomolecular analysis. The TA fragments obtained with the minimally-invasive needle biopsy technique is enough to perform all the histopathological and biomolecular evaluations useful to monitor a clinical trial on DM1 patients.

  18. Tibialis anterior muscle needle biopsy and sensitive biomolecular methods: a useful tool in myotonic dystrophy type 1.

    Science.gov (United States)

    Iachettini, S; Valaperta, R; Marchesi, A; Perfetti, A; Cuomo, G; Fossati, B; Vaienti, L; Costa, E; Meola, G; Cardani, R

    2015-10-26

    Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by a CTG repeat expansion in 3'UTR of DMPK gene. This mutation causes accumulation of toxic RNA in nuclear foci leading to splicing misregulation of specific genes. In view of future clinical trials with antisense oligonucleotides in DM1 patients, it is important to set up sensitive and minimally-invasive tools to monitor the efficacy of treatments on skeletal muscle. A tibialis anterior (TA) muscle sample of about 60 mg was obtained from 5 DM1 patients and 5 healthy subjects through a needle biopsy. A fragment of about 40 mg was used for histological examination and a fragment of about 20 mg was used for biomolecular analysis. The TA fragments obtained with the minimally-invasive needle biopsy technique is enough to perform all the histopathological and biomolecular evaluations useful to monitor a clinical trial on DM1 patients.

  19. System and method for determining an ammonia generation rate in a three-way catalyst

    Science.gov (United States)

    Sun, Min; Perry, Kevin L; Kim, Chang H

    2014-12-30

    A system according to the principles of the present disclosure includes a rate determination module, a storage level determination module, and an air/fuel ratio control module. The rate determination module determines an ammonia generation rate in a three-way catalyst based on a reaction efficiency and a reactant level. The storage level determination module determines an ammonia storage level in a selective catalytic reduction (SCR) catalyst positioned downstream from the three-way catalyst based on the ammonia generation rate. The air/fuel ratio control module controls an air/fuel ratio of an engine based on the ammonia storage level.

  20. Binder model system to be used for determination of prepolymer functionality

    Science.gov (United States)

    Martinelli, F. J.; Hodgkin, J. H.

    1971-01-01

    Development of a method for determining the functionality distribution of prepolymers used for rocket binders is discussed. Research has been concerned with accurately determining the gel point of a model polyester system containing a single trifunctional crosslinker, and the application of these methods to more complicated model systems containing a second trifunctional crosslinker, monofunctional ingredients, or a higher functionality crosslinker. Correlations of observed with theoretical gel points for these systems would allow the methods to be applied directly to prepolymers.

  1. ARTICLES: Second-generation lidar system for determining the distance to the Moon

    Science.gov (United States)

    Kokurin, Yu L.; Kurbasov, V. V.; Lobanov, V. F.; Sukhanovskiĭ, A. N.

    1983-06-01

    A description is given of a lidar system for determination of the distance to the Moon. This system has a resolution of 1 nsec and it consists of a laser transmitter, a photodetector, a pulse processing subsystem, as well as timing and guiding subsystems. The system has been in operation since 1978. The parameters of the subsystems and the errors in the determination of time intervals are discussed.

  2. Second-generation lidar system for determining the distance to the moon

    Science.gov (United States)

    Kokurin, Iu. L.; Kurbasov, V. V.; Lobanov, V. F.; Sukhanovskii, A. N.

    1983-06-01

    A description is given of a lidar system for determination of the distance to the moon. This system has a resolution of 1 nsec and it consists of a laser transmitter, a photodetector, a pulse processing subsystem, as well as timing and guiding subsystems. The system has been in operation since 1978. The parameters of the subsystems and the errors in the determination of time intervals are discussed.

  3. Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications

    Science.gov (United States)

    Chirvi, Sajal

    Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

  4. Biomolecular interactions and tools for their recognition: focus on the quartz crystal microbalance and its diverse surface chemistries and applications.

    Science.gov (United States)

    Cheng, Cathy I; Chang, Yi-Pin; Chu, Yen-Ho

    2012-03-07

    Interactions between molecules are ubiquitous and occur in our bodies, the food we eat, the air we breathe, and myriad additional contexts. Although numerous tools are available for the recognition of biomolecular interactions, such tools are often limited in their sensitivity, expensive, and difficult to modify for various uses. In contrast, the quartz crystal microbalance (QCM) has sub-nanogram detection capabilities, is label-free, is inexpensive to create, and can be readily modified with a number of diverse surface chemistries to detect and characterize diverse interactions. To maximize the versatility of the QCM, scientists need to know available methods by which QCM surfaces can be modified. Therefore, in addition to summarizing the various tools currently used for biomolecular recognition, explicating the fundamental principles of the QCM as a tool for biomolecular recognition, and comparing the QCM with other acoustic sensors, we systematically review the numerous types of surface chemistries-including hydrophobic bonds, ionic bonds, hydrogen bonds, self-assembled monolayers, plasma-polymerized films, photochemistry, and sensing ionic liquids-used to functionalize QCMs for various purposes. We also review the QCM's diverse applications, which include the detection of gaseous species, detection of carbohydrates, detection of nucleic acids, detection of non-enzymatic proteins, characterization of enzymatic activity, detection of antigens and antibodies, detection of cells, and detection of drugs. Finally, we discuss the ultimate goals of and potential barriers to the development of future QCMs.

  5. A Teaching and Learning Sequence about the Interplay of Chance and Determinism in Nonlinear Systems

    Science.gov (United States)

    Stavrou, D.; Duit, R.; Komorek, M.

    2008-01-01

    A teaching and learning sequence aimed at introducing upper secondary school students to the interplay between chance and determinism in nonlinear systems is presented. Three experiments concerning nonlinear systems (deterministic chaos, self-organization and fractals) and one experiment concerning linear systems are introduced. Thirty upper…

  6. 76 FR 61740 - Pension Systems Corporation, Sherman Oaks, CA; Notice of Affirmative Determination Regarding...

    Science.gov (United States)

    2011-10-05

    ... Employment and Training Administration Pension Systems Corporation, Sherman Oaks, CA; Notice of Affirmative... apply for Trade Adjustment Assistance (TAA) applicable to workers and former workers of Pension Systems Corporation, Sherman Oaks, California (Pension Systems). The negative determination was issued on July...

  7. 75 FR 61509 - Notice of Issuance of Final Determination Concerning Solar Photovoltaic Panel Systems

    Science.gov (United States)

    2010-10-05

    ... Photovoltaic Panel Systems AGENCY: U.S. Customs and Border Protection, Department of Homeland Security. ACTION..., Trade Agreements Act of 1979; Country of Origin of solar photovoltaic panel system; substantial... determination concerns the country of origin of certain photovoltaic panel systems that Solyndra may sell to...

  8. Wireless Location Determination for Mobile Objects Based on GSM in Intelligent Transportation Systems

    Institute of Scientific and Technical Information of China (English)

    徐志扬; 施鹏飞

    2003-01-01

    The mobile object (MO) location determination technologies which can be used in intelligent transportation system (ITS) are studied in this paper. The principles and characteristics of wireless location determination technologies are introduced and the characteristics of GSM useful for location determination are also summarized. An experimental positioning system based on GSM is proposed, and the architecture is described. TOA method based on GSM signals and TDOA method are used in the experimental system. Moreover, the methods are simulated. The performance of the positioning methods is assessed in the simulation environment, and the accuracy for 67% mobile stations (MS) is 70m in urban areas.

  9. Report on result 1998. Research and development on fusion area. Part 3 (biomolecular mechanism and design); 1998 nendo seika hokokusho. Yugo ryoiki kenkyu kaihatsu daisan bunsatsu (bimolecular mechanism and design)

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-03-01

    An organism is a molecular mechanical system consisting of nucleic acid, peptide and protein having a self-forming and a self-repairing function. For the purpose of creating cells, tissues and molecular mechanism alternating these biological functions, their basic technology was developed. Concretely, studies were made on three-dimensional cellular structural module engineering and biomolecular mechanism and design. Studies on biological soft tissue resulted in success by giving atmospheric glow discharge treatment to the inner surface of a tubular PVC. An artificial vitreous body was created using PVA hydrogels. In addition, liver cells were successfully cultured for the first time in the world. Studies on biological hard tissue revealed that osteopontin plays a role of a trigger for the initial differentiation of the osteoblast cell. Further, a basic experiment was carried out on the initial response of the cartilage cell. In the research on the molecular mechanism, examination was made on the mechanism of a double-head molecular motor. Examination was also made on the adjustment of the hydrogenase LB film as an electricity/hydrogen energy conversion element and on the biomolecular mechanism and design. (NEDO)

  10. Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

    Directory of Open Access Journals (Sweden)

    Hassan Taghipour

    2013-01-01

    Full Text Available Solving some mathematical problems such as NP-complete problems by conventional silicon-based computers is problematic and takes so long time. DNA computing is an alternative method of computing which uses DNA molecules for computing purposes. DNA computers have massive degrees of parallel processing capability. The massive parallel processing characteristic of DNA computers is of particular interest in solving NP-complete and hard combinatorial problems. NP-complete problems such as knapsack problem and other hard combinatorial problems can be easily solved by DNA computers in a very short period of time comparing to conventional silicon-based computers. Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem. At first, a biomolecular solution space was constructed by using appropriate DNA memory complexes. Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.

  11. A coarse-grained model for the simulations of biomolecular interactions in cellular environments

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao, E-mail: yinghao.wu@einstein.yu.edu [Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461 (United States)

    2014-02-07

    The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments.

  12. Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition.

    Science.gov (United States)

    Yu, Hua; Zhou, Peng; Deng, Maolin; Shang, Zhicai

    2014-07-28

    Protein-peptide interactions are prevalent and play essential roles in many living activities. Peptides recognize their protein partners by direct nonbonded interactions and indirect adjustment of conformations. Although processes of protein-peptide recognition have been comprehensively studied in both sequences and structures recently, flexibility of peptides and the configuration entropy penalty in recognition did not get enough attention. In this study, 20 protein-peptide complexes and their corresponding unbound peptides were investigated by molecular dynamics simulations. Energy analysis revealed that configurational entropy penalty introduced by restriction of the degrees of freedom of peptides in indirect readout process of protein-peptide recognition is significant. Configurational entropy penalty has become the main content of the indirect readout energy in protein-peptide recognition instead of deformation energy which is the main source of the indirect readout energy in classical biomolecular recognition phenomena, such as protein-DNA binding. These results provide us a better understanding of protein-peptide recognition and give us some implications in peptide ligand design.

  13. Nanoscale Biomolecular Detection Limit for Gold Nanoparticles Based on Near-Infrared Response

    Directory of Open Access Journals (Sweden)

    Mario D’Acunto

    2012-01-01

    Full Text Available Gold nanoparticles have been widely used during the past few years in various technical and biomedical applications. In particular, the resonance optical properties of nanometer-sized particles have been employed to design biochips and biosensors used as analytical tools. The optical properties of nonfunctionalized gold nanoparticles and core-gold nanoshells play a crucial role for the design of biosensors where gold surface is used as a sensing component. Gold nanoparticles exhibit excellent optical tunability at visible and near-infrared frequencies leading to sharp peaks in their spectral extinction. In this paper, we study how the optical properties of gold nanoparticles and core-gold nanoshells are changed as a function of different sizes, shapes, composition, and biomolecular coating with characteristic shifts towards the near-infrared region. We show that the optical tenability can be carefully tailored for particle sizes falling in the range 100–150 nm. The results should improve the design of sensors working at the detection limit.

  14. Biomolecular characterization of the levansucrase of Erwinia amylovora, a promising biocatalyst for the synthesis of fructooligosaccharides.

    Science.gov (United States)

    Caputi, Lorenzo; Nepogodiev, Sergey A; Malnoy, Mickael; Rejzek, Martin; Field, Robert A; Benini, Stefano

    2013-12-18

    Erwinia amylovora is a plant pathogen that affects Rosaceae, such as apple and pear. In E. amylovora the fructans, produced by the action of a levansucrase (EaLsc), play a role in virulence and biofilm formation. Fructans are bioactive compounds, displaying health-promoting properties in their own right. Their use as food and feed supplements is increasing. In this study, we investigated the biomolecular properties of EaLsc using HPAEC-PAD, MALDI-TOF MS, and spectrophotometric assays. The enzyme, which was heterologously expressed in Escherichia coli in high yield, was shown to produce mainly fructooligosaccharides (FOSs) with a degree of polymerization between 3 and 6. The kinetic properties of EaLsc were similar to those of other phylogenetically related Gram-negative bacteria, but the good yield of FOSs, the product spectrum, and the straightforward production of the enzyme suggest that EaLsc is an interesting biocatalyst for future studies aimed at producing tailor-made fructans.

  15. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires

    Science.gov (United States)

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao

    2015-05-01

    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two peripheral ubiquinone moieties and solvents effects are limited and mostly depend on the nature of solvents. The DFT calculations for the first time indicate the intensity of the electronic communications during the redox processes rely on the molecular orbital elements VL for electron transfer (half of the energy splitting of the LUMO and LUMO+1), which is could be affected by the bridges linkers. The DFT calculations also demonstrates the effect of solvents on the latter two-electron transfer of Bis-CoQ0s is more significant than the former two electrons transfer as the observed electrochemical behaviors of three Bis-CoQ0s. In addition, the electrochemistry and theoretical calculations reveal the intramolecular electronic communications vary in the four-electron redox processes of three Bis-CoQ0s.

  16. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis.

    Science.gov (United States)

    Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T

    2016-01-01

    The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

  17. Review of Transducer Principles for Label-Free Biomolecular Interaction Analysis

    Directory of Open Access Journals (Sweden)

    Janos Vörös

    2011-07-01

    Full Text Available Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM and the film bulk acoustic resonator (FBAR, calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.

  18. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.

    Science.gov (United States)

    Pardee, Keith; Green, Alexander A; Takahashi, Melissa K; Braff, Dana; Lambert, Guillaume; Lee, Jeong Wook; Ferrante, Tom; Ma, Duo; Donghia, Nina; Fan, Melina; Daringer, Nichole M; Bosch, Irene; Dudley, Dawn M; O'Connor, David H; Gehrke, Lee; Collins, James J

    2016-05-19

    The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. PAPERCLIP.

  19. Biomolecular Nano-Flow-Sensor to Measure Near-Surface Flow

    Directory of Open Access Journals (Sweden)

    Noji Hiroyuki

    2009-01-01

    Full Text Available Abstract We have proposed and experimentally demonstrated that the measurement of the near-surface flow at the interface between a liquid and solid using a 10 nm-sized biomolecular motor of F1-ATPase as a nano-flow-sensor. For this purpose, we developed a microfluidic test-bed chip to precisely control the liquid flow acting on the F1-ATPase. In order to visualize the rotation of F1-ATPase, several hundreds nanometer-sized particle was immobilized at the rotational axis of F1-ATPase to enhance the rotation to be detected by optical microscopy. The rotational motion of F1-ATPase, which was immobilized on an inner surface of the test-bed chip, was measured to obtain the correlation between the near-surface flow and the rotation speed of F1-ATPase. As a result, we obtained the relationship that the rotation speed of F1-ATPase was linearly decelerated with increasing flow velocity. The mechanism of the correlation between the rotation speed and the near-surface flow remains unclear, however the concept to use biomolecule as a nano-flow-sensor was proofed successfully. (See supplementary material 1 Electronic supplementary material The online version of this article (doi:10.1007/s11671-009-9479-3 contains supplementary material, which is available to authorized users. Click here for file

  20. Drug Transport Microdevice Mimicking an Idealized Nanoscale Bio-molecular Motor

    Institute of Scientific and Technical Information of China (English)

    Jae Hwan Lee; Ramana M. Pidaparti

    2011-01-01

    Molecular motors are nature's nano-devices and the essential agents of movement that are an integral part of many living organisms.The supramolecular motor,called Nuclear Pore Complex (NPC),controls the transport of all cellular material between the cytoplasm and the nucleus that occurs naturally in biological cells of many organisms.In order to understand the design characteristics of the NPC,we developed a microdevice for drug/fluidic transport mimicking the coarse-grained representation of the NPC geometry through computational fluid dynamic analysis and optimization.Specifically,the role of the central plug in active fluidic/particle transport and passive transport (without central plug) was investigated.Results of flow rate,pressure and velocity profiles obtained from the models indicate that the central plug plays a major role in transport through this biomolecular machine.The results of this investigation show that fluidic transport and flow passages are important factors in designing NPC based nano- and micro-devices for drug delivery.

  1. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.

    Science.gov (United States)

    Li, Hongchun; Chang, Yuan-Yu; Yang, Lee-Wei; Bahar, Ivet

    2016-01-04

    Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0 http://gnmdb.csb.pitt.edu/, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.

  2. Colloid-in-liquid crystal gels that respond to biomolecular interactions.

    Science.gov (United States)

    Agarwal, Ankit; Sidiq, Sumyra; Setia, Shilpa; Bukusoglu, Emre; de Pablo, Juan J; Pal, Santanu Kumar; Abbott, Nicholas L

    2013-08-26

    This paper advances the design of stimuli-responsive materials based on colloidal particles dispersed in liquid crystals (LCs). Specifically, thin films of colloid-in-liquid crystal (CLC) gels undergo easily visualized ordering transitions in response to reversible and irreversible (enzymatic) biomolecular interactions occurring at the aqueous interfaces of the gels. In particular, LC ordering transitions can propagate across the entire thickness of the gels. However, confinement of the LC to small domains with lateral sizes of ∼10 μm does change the nature of the anchoring transitions, as compared to films of pure LC, due to the effects of confinement on the elastic energy stored in the LC. The effects of confinement are also observed to cause the response of individual domains of the LC within the CLC gel to vary significantly from one to another, indicating that manipulation of LC domain size and shape can provide the basis of a general and facile method to tune the response of these LC-based physical gels to interfacial phenomena. Overall, the results presented in this paper establish that CLC gels offer a promising approach to the preparation of self-supporting, LC-based stimuli-responsive materials.

  3. High-Throughput, Protein-Targeted Biomolecular Detection Using Frequency-Domain Faraday Rotation Spectroscopy.

    Science.gov (United States)

    Murdock, Richard J; Putnam, Shawn A; Das, Soumen; Gupta, Ankur; Chase, Elyse D Z; Seal, Sudipta

    2017-01-16

    A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL(-1) and broad detection range of 10 pg mL(-1) ≲ cBSA ≲ 100 µg mL(-1) are observed. Combining this technique with predictive analyte binding models quantifies (within an order of magnitude) the number of active binding sites on functionalized MNPs. Comparative enzyme-linked immunosorbent assay (ELISA) studies are conducted, reproducing the manufacturer advertised BSA ELISA detection limits from 1 ng mL(-1) ≲ cBSA ≲ 500 ng mL(-1) . In addition to the increased sensitivity, broader detection range, and similar specificity, fd-FRS can be conducted in less than ≈30 min, compared to ≈4 h with ELISA. Thus, fd-FRS is shown to be a sensitive optical technique with potential to become an efficient diagnostic in the chemical and biomolecular sciences.

  4. Liquid-filled transient pressure measuring systems: A method for determining frequency response

    Science.gov (United States)

    Anderson, R. C.; Englund, D. R., Jr.

    1971-01-01

    An equation is given and experimentally verified for computing the resonant frequency of liquid-filled transient pressure measuring systems. Resonant frequencies of 100 to 1000 Hz are typical of those systems tested. The effect of noncondensable gas bubbles on system response is described. A method for determining transducer volumetric compliance is presented. An example system is described and analyzed to demonstrate the use of the theory.

  5. Plug-and-Play Compatibility for CubeSat Attitude Determination and Control Systems Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The development of Plug-and-play Compatibility for CubeSat Attitude Determination and Control Systems (ADACS) is proposed. Existing Maryland Aerospace (MAI) ADACS...

  6. Determination of principles of the unified state system for ecomonitoring an example of Carpathian region

    Directory of Open Access Journals (Sweden)

    Mishhenko L.V.

    2010-06-01

    Full Text Available The method and program of environmental studies to determine the principles of a unified environmental monitoring system for the Ukraine in general, regions, provinces, districts and cities.

  7. System and method for determining the net output torque from a waste heat recovery system

    Energy Technology Data Exchange (ETDEWEB)

    Tricaud, Christophe; Ernst, Timothy C.; Zigan, James A.

    2016-12-13

    The disclosure provides a waste heat recovery system with a system and method for calculation of the net output torque from the waste heat recovery system. The calculation uses inputs from existing pressure and speed sensors to create a virtual pump torque sensor and a virtual expander torque sensor, and uses these sensors to provide an accurate net torque output from the WHR system.

  8. Portable LIBS system for determining the composition of multilayer structures on objects of cultural value

    Energy Technology Data Exchange (ETDEWEB)

    Moreira Osorio, Lesther [IMRE-Havana University, Vedado 10400, Havana (Cuba); Ponce Cabrera, Luis V; Arronte Garcia, Miguel A; Flores Reyes, Teresa [CICATA-IPN, km 14.5 Carretera Tampico Puerto industrial, Altamira 89600, Tamps (Mexico); Ravelo, Ivette, E-mail: lesther.moreira@gmail.com [National Center for Conservation, Restoration and Museology (CENCREM) (Cuba)

    2011-01-01

    This study presents the use of a portable Laser Induced Breakdown Spectroscopy (LIBS) prototype for determining the elemental composition of a metal jug. The system includes emission from a multiuse Q-switched Nd:YAG laser. By sampling at different points, the surface composition is determined. Furthermore, the presence of two layers of Pb and Cu and their thicknesses are determined through in-depth analysis.

  9. Ion implantation system and process for ultrasensitive determination of target isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Farmer, III, Orville T.; Liezers, Martin

    2016-09-13

    A system and process are disclosed for ultrasensitive determination of target isotopes of analytical interest in a sample. Target isotopes may be implanted in an implant area on a high-purity substrate to pre-concentrate the target isotopes free of contaminants. A known quantity of a tracer isotope may also be implanted. Target isotopes and tracer isotopes may be determined in a mass spectrometer. The present invention provides ultrasensitive determination of target isotopes in the sample.

  10. Luminol-potassium permanganate chemiluminescence system for the determination of three anthracycline antibiotics

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Objective To establish a flow-injection chemiluminescence method for the determination of doxorubicin,epirubicin and mitoxantrone and study its reaction mechanism.Methods In alkaline medium,chemiluminescence of luminol-potassium permanganate system could be inhibited obviously by anthracycline antibiotics.Combined with flow-injection technique,a new chemiluminescence method for determining the anthracycline antibiotics was set up.The chemiluminescence mechanism of the luminol-potassium permanganate system w...

  11. Biomolecular Mechanisms of Adaptive Reflectance and Related Biophotonic Systems in Molluscs

    Science.gov (United States)

    2015-01-09

    lightweight solar cells, IR detectors, and recovery of waste heat through thermal photovoltaics. Accordion-like folds in the cell membrane filled with unique...ADDRESS (ES) U.S. Army Research Office P.O. Box 12211 Research Triangle Park , NC 27709-2211 Squid, Photonics; Proteins; Reflectin; Camouflage...improvements in lightweight solar cells, IR detectors, and recovery of waste heat through thermal photovoltaics. Accordion-like folds in the cell membrane

  12. PELE web server: atomistic study of biomolecular systems at your fingertips.

    Science.gov (United States)

    Madadkar-Sobhani, Armin; Guallar, Victor

    2013-07-01

    PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

  13. Proton Solvation and Transport in Aqueous and Biomolecular Systems: Insights from Computer Simulations

    OpenAIRE

    Swanson, Jessica M. J.; Maupin, C. Mark; Chen, Hanning; Petersen, Matt K.; Xu, Jiancong; Wu, Yujie; Voth, Gregory A.

    2007-01-01

    The excess proton in aqueous media plays a pivotal role in many fundamental chemical (e.g., acid-base chemistry) and biological (e.g., bioenergetics and enzyme catalysis) processes. Understanding the hydrated proton is, therefore, crucial for chemistry, biology, and materials sciences. Although well studied for over 200 years, excess proton solvation and transport remains to this day mysterious, surprising, and perhaps even misunderstood. In this feature article various efforts to address thi...

  14. Terahertz Solitons in Biomolecular Systems and their Excitation by External Electromagnetic Field

    Directory of Open Access Journals (Sweden)

    Bugay А.N.

    2015-01-01

    Full Text Available Nonlinear dynamics of charge and acoustic excitations in cellular microtubules is considered. Different types of nonlinear solitary waves were studied taking account for dissipation. The mechanism of electro-acoustic pulse excitation by external electromagnetic field of terahertz frequency is recognized.

  15. Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems

    NARCIS (Netherlands)

    Vreede, J.; Wolf, M.G.; de Leeuw, S.W.; Bolhuis, P.G.

    2009-01-01

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in a

  16. Detection systems for mass spectrometry imaging: a perspective on novel developments with a focus on active pixel detectors

    NARCIS (Netherlands)

    Jungmann, JH; Heeren, R.M.A.

    2013-01-01

    Instrumental developments for imaging and individual particle detection for biomolecular mass spectrometry (imaging) and fundamental atomic and molecular physics studies are reviewed. Ion-counting detectors, array detection systems and highmass detectors for mass spectrometry (imaging) are treated.

  17. Design and application of single-antenna GPS/accelerometers attitude determination system

    Institute of Scientific and Technical Information of China (English)

    He Jie; Huang Xianlin; Wang Guofeng

    2008-01-01

    In view of the problem that the current single-antenna GPS attitude determination system can only determine the body attitude when the sideslip angle is zero and the multiantenna GPS/SINS integrated navigation system is of large volume, high cost, and complex structure, this approach is presented to determine the attitude based on vector space with single-antenna GPS and accelerometers in the micro inertial measurement unit (MIMU).It can provide real-time and accurate attitude information. Subsequently, the single-antenna GPS/SINS integrated navigation system is designed based on the combination of position, velocity, and attitude. Finally the semi-physical simulations of single-antenna GPS attitude determination system and single-antenna GPS/SINS integrated navigation system are carried out. The simulation results, based on measured data, show that the single-antenna GPS/SINS system can provide more accurate navigation information compared to the GPS/SINS system, based on the combination of position and velocity. Furthermore, the single-antenna GPS/SINS system is characteristic of lower cost and simpler structure. It provides the basis for the application of a single-antenna GPS/SINS integrated navigation system in a micro aerial vehicle (MAV).

  18. Noise-spectroscopy of multiqubit systems: Determining all their parameters by applying an external classical noise

    Energy Technology Data Exchange (ETDEWEB)

    Savel' ev, S., E-mail: S.Saveliev@lboro.ac.uk [Department of Physics, Loughborough University, Leicestershire LE11 3TU (United Kingdom); Advanced Science Institute, RIKEN, Wako-shi, Saitama 351-0198 (Japan); Zagoskin, A.M. [Department of Physics, Loughborough University, Leicestershire LE11 3TU (United Kingdom); Advanced Science Institute, RIKEN, Wako-shi, Saitama 351-0198 (Japan); Omelyanchouk, A.N. [Advanced Science Institute, RIKEN, Wako-shi, Saitama 351-0198 (Japan); B. Verkin Institute for Low Temperature Physics and Engineering, 61103 Kharkov (Ukraine); Nori, Franco [Advanced Science Institute, RIKEN, Wako-shi, Saitama 351-0198 (Japan); Physics Department, University of Michigan, Ann Arbor, MI 48109-1040 (United States)

    2010-10-05

    Imagine that you have several sets of two coupled qubits, but you do not know the parameters of their Hamitonians. How to determine these without resorting to the usual spectroscopy approach to the problem? Based on numerical modeling, we show that all the parameters of a system of two coupled qubits can be determined by applying to it an external classical noise and analyzing the Fourier spectrum of the elements of the system's density matrix. In particular, the interlevel spacings as well as the strength and sign of the qubit-qubit coupling can be determined this way.

  19. Methods to Determine Recommended Feeder-Wide Advanced Inverter Settings for Improving Distribution System Performance

    Energy Technology Data Exchange (ETDEWEB)

    Rylander, Matthew; Reno, Matthew J.; Quiroz, Jimmy E.; Ding, Fei; Li, Huijuan; Broderick, Robert J.; Mather, Barry; Smith, Jeff

    2016-11-21

    This paper describes methods that a distribution engineer could use to determine advanced inverter settings to improve distribution system performance. These settings are for fixed power factor, volt-var, and volt-watt functionality. Depending on the level of detail that is desired, different methods are proposed to determine single settings applicable for all advanced inverters on a feeder or unique settings for each individual inverter. Seven distinctly different utility distribution feeders are analyzed to simulate the potential benefit in terms of hosting capacity, system losses, and reactive power attained with each method to determine the advanced inverter settings.

  20. Automatic system for the determination of metals by anodic stripping potentiometry in non-deaerated samples

    OpenAIRE

    1990-01-01

    An automatic system for the determination of Zn, Cd, Pb and Cu by anodic stripping potentiometry using the oxygen dissolved in the sample as oxidant is reported. The system relies on the use of a PC-compatible computer for instrumental control and data acquisition and processing.

  1. 76 FR 29765 - Determination of System Attributes for the Tracking and Tracing of Prescription Drugs; Reopening...

    Science.gov (United States)

    2011-05-23

    ... the Division of Dockets Management (HFA- 305), Food and Drug Administration, 5630 Fishers Lane, rm... possible approaches to developing a track-and-trace system and (2) input from supply chain partners on... HUMAN SERVICES Food and Drug Administration Determination of System Attributes for the Tracking...

  2. A new method for the determination of particulate contamination levels for surface cleanliness of fluid systems

    Science.gov (United States)

    1969-01-01

    Levels of contamination in fluid systems can be determined by a definition of a particle by a mathematical model, a method for calculating the tolerance limits of contamination, and an estimation of the probability that the contamination on the surface will migrate with the fluid in the system.

  3. The implications for information system design of how health care costs are determined.

    Science.gov (United States)

    Ehreth, J

    1996-03-01

    As the costs of health care assume increasing importance in national health policy, information systems will be required to supply better information about how costs are generated and how resources are distributed. Costs, as determined by accounting systems, often are inadequate for policy analysis because they represent resources consumed (expenditures) to produce given outputs but do not measure forgone alternative uses of the resources (opportunity costs). To accommodate cost studies at the program level and the system level, relational information systems must be developed that allow costs to be summed across individuals to determine an organization's costs, across providers to determine an individual patient's costs, and across both to determine system and population costs. Program level studies require that cost variables be grouped into variable costs that are tied to changes in volume of output and fixed costs that are allocated rationally. Data sources for program-level analyses are organizational financial statements, cost center accounting records, Medicare cost reports, American Hospital Association surveys, and the Department of Veterans Affairs (VA) cost distribution files. System-level studies are performed to predict future costs and to compare costs of alternative modes of treatment. System-level analyses aggregate all costs associated with individuals to produce population-based costs. Data sources for system-level analyses include insurance claims;n Medicare files; hospital billing records; and VA inpatient, outpatient, and management databases. Future cost studies will require the assessment of costs from all providers, regardless of organizational membership status, for all individuals in defined populations.

  4. 40 CFR 63.3554 - How do I determine the emission capture system efficiency?

    Science.gov (United States)

    2010-07-01

    ... capture system meets the criteria in Method 204 of appendix M to 40 CFR part 51 for a PTE and directs all... system efficiency? 63.3554 Section 63.3554 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Requirements for the Control Efficiency/outlet Concentration Option § 63.3554 How do I determine the...

  5. Morbillivirus infection in cetaceans stranded along the Italian coastline: pathological, immunohistochemical and biomolecular findings.

    Science.gov (United States)

    Di Guardo, Giovanni; Di Francesco, Cristina Esmeralda; Eleni, Claudia; Cocumelli, Cristiano; Scholl, Francesco; Casalone, Cristina; Peletto, Simone; Mignone, Walter; Tittarelli, Cristiana; Di Nocera, Fabio; Leonardi, Leonardo; Fernández, Antonio; Marcer, Federica; Mazzariol, Sandro

    2013-02-01

    Morbilliviruses are recognized as biological agents highly impacting the health and conservation status of free-ranging cetaceans worldwide, as clearly exemplified by the two Dolphin Morbillivirus (DMV) epidemics of 1990-1992 and 2006-2008 among Mediterranean striped dolphins (Stenella coeruleoalba). After these two epidemics, morbilliviral infection (MI) cases with peculiar neurobiological features were reported in striped dolphins stranded along the Spanish coastline. Affected cetaceans showed a subacute-to-chronic, non-suppurative encephalitis, with brain lesions strongly resembling those found in human "subacute sclerosing panencephalitis" and "old dog encephalitis". Brain was the only tissue in which morbilliviral antigen and/or genome could be detected. Beside a case of morbilliviral encephalitis in a striped dolphin's calf stranded in 2009, we observed 5 additional MI cases in 2 striped dolphins, 1 bottlenose dolphin (Tursiops truncatus) and 2 fin whales (Balaenoptera physalus), all stranded in 2011 along the Italian coastline. Noteworthy, 3 of these animals (2 striped dolphins and 1 bottlenose dolphin) showed immunohistochemical (IHC) and/or biomolecular (PCR) evidence of morbilliviral antigen and/or genome exclusively in their brain, with 1 striped dolphin and 1 bottlenose dolphin also exhibiting a non-suppurative encephalitis. Furthermore, simultaneous IHC and PCR evidence of a Toxoplasma gondii coinfection was obtained in 1 fin whale. The above results are consistent with those reported in striped dolphins after the two MI epidemics of 1990-92 and 2006-2008, with evidence of morbilliviral antigen and/or genome being found exclusively in the brain tissue from affected animals.

  6. Immunohistochemical Study to Evaluate the Prognostic Significance of Four Biomolecular Markers in Radiotherapy of Nasopharyngeal Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yeon Joo; Lee, Seung Hee; Wu, Hong Gyun; Go, Heoun Jeong; Jeon, Yoon Kyung [Seoul National University College of Medicine, Seoul (Korea, Republic of)

    2010-11-15

    We performed an immunohistochemical study with pre-treatment biopsy specimens to evaluate the prognostic significance of four biomolecular markers which can be used as a predictive assay for radiotherapy (RT) treatment of nasopharyngeal carcinoma (NPC). From January 1998 through December 2006, 68 patients were histologically diagnosed as non-metastatic NPC and treated by RT. Only 38 patients had the paraffin block for the immunohistochemical study. Thirty-one patients had undifferentiated carcinoma and 7 patients had squamous cell carcinoma. Thirty two patients (84%) had advanced stage NPC (2002 AJCC Stage III{approx}IV). Immunohistochemical staining was performed for Met, COX-2, nm23-H1, and epidermal growth factor receptor (EGFR) expression using routine methods. The median follow-up time was 30 months (range, 11 to 83 months) for all patients, and 39 months (range, 19 to 83 months) for surviving patients. The 5-year overall survival (OS) rate of the patients with high Met extent ({>=}50%) was significantly lower than that of the patients with low Met extent (48% vs. 84%, p=0.02). In addition, Met extent was also a significant prognostic factor in multivariate analysis (p=0.01). No correlation was observed between Met extent and T stage, N stage, stage group, gender, age, and the response to chemotherapy or RT. Met extent showed moderate correlation with COX-2 expression (Pearson coefficient 0.496, p<0.01), but COX-2 expression did not affect OS. Neither nm23-H1 or EGFR expression was a prognostic factor for OS in this study. High Met extent ({>=}50%) might be an independent prognostic factor that predicts poor OS in NPC treated with RT.

  7. Evolução biomolecular homoquiral: a origem e a amplificação da quiralidade nas moléculas da vida Homochiral biomolecular evolution: the origin and the amplification of chirality in life molecules

    Directory of Open Access Journals (Sweden)

    José Augusto R. Rodrigues

    2010-01-01

    Full Text Available The fact that biologically relevant molecules exist only as one of the two enantiomers is a fascinating example of complete symmetry breaking of chirality and has long intrigued our curiosity. The origin of this selective chirality has remained a fundamental enigma with regard to the origin of life since the time of Pasteur, 160 years ago. The symmetry breaking processes, which include autocatalytic crystallization, asymmetric autocatalysis, spontaneous crystallization, adsorption and polymerization of amino acids on mineral surfaces, provide new insights into the origin of biomolecular homochirality.

  8. Financial systems: essays on the cultural determinants and the relevance for economic development

    OpenAIRE

    Gheeraert, Laurent

    2009-01-01

    The thesis analyzes macro-economic determinants and roles of financial sector development. The literature argues that the size and efficiency of both banking systems and financial markets - the two major components of a financial system - matter for economic development. In the same vein, the quality of financial institutions and regulations are instrumental in the construction of a strong financial system. We study several aspects of financial sector development in relation to three recent p...

  9. Determining Component Probability using Problem Report Data for Ground Systems used in Manned Space Flight

    Science.gov (United States)

    Monaghan, Mark W.; Gillespie, Amanda M.

    2013-01-01

    During the shuttle era NASA utilized a failure reporting system called the Problem Reporting and Corrective Action (PRACA) it purpose was to identify and track system non-conformance. The PRACA system over the years evolved from a relatively nominal way to identify system problems to a very complex tracking and report generating data base. The PRACA system became the primary method to categorize any and all anomalies from corrosion to catastrophic failure. The systems documented in the PRACA system range from flight hardware to ground or facility support equipment. While the PRACA system is complex, it does possess all the failure modes, times of occurrence, length of system delay, parts repaired or replaced, and corrective action performed. The difficulty is mining the data then to utilize that data in order to estimate component, Line Replaceable Unit (LRU), and system reliability analysis metrics. In this paper, we identify a methodology to categorize qualitative data from the ground system PRACA data base for common ground or facility support equipment. Then utilizing a heuristic developed for review of the PRACA data determine what reports identify a credible failure. These data are the used to determine inter-arrival times to perform an estimation of a metric for repairable component-or LRU reliability. This analysis is used to determine failure modes of the equipment, determine the probability of the component failure mode, and support various quantitative differing techniques for performing repairable system analysis. The result is that an effective and concise estimate of components used in manned space flight operations. The advantage is the components or LRU's are evaluated in the same environment and condition that occurs during the launch process.

  10. Accuracy analysis of a mobile tracking system for angular position determination of flying targets

    Science.gov (United States)

    Walther, Andreas; Buske, Ivo; Riede, Wolfgang

    2016-10-01

    Lasers arouse an increasing interest in remote sensing applications. In order to deliver as much as possible of the available laser power onto a flying object the subsystems of a beam control system have to operate precisely together. One important subsystem is responsible for determination of the target's angular position. Here, we focus on an optical system for measuring precisely the angular position of flying objects. We designed this subunit of a beam control system exclusively from readily available commercial-off-the-shelf components. Two industrial cameras were used for angle measuring and for guiding the system to the position of the flying object. Both cameras are mounted on a modified astronomical mount with high-precision angle encoders. To achieve a high accuracy we temporally synchronize the acquisition of the angle from the pan tilt unit with the exposure of the camera. Therefore, a FPGA-based readout device for the rotary encoders was designed and implemented. Additionally, we determined and evaluated the influence of the distortion of the lenses to the measurement. We investigated various scenarios to determine the accuracy and the limitations of our system for angular position determination of flying targets. Performance tests were taken indoor and outdoor at our test sites. A target can be mounted on a fast moving linear stage. The position of this linear stage is continuously read out by a high resolution encoder so we know the target's position with a dynamic accuracy in the range of a few μm. With this setup we evaluated the spatial resolution of our tracking system. We showed that the presented system can determine the angular position of fast flying objects with an uncertainty of only 2 μrad RMS. With this mobile tracking system for angular position determination of flying targets we designed an accurate cost-efficient opportunity for further developments.

  11. Study on Technique of Surface Plasmon Resonance Imaging Sensing for Biomolecular Interaction

    Institute of Scientific and Technical Information of China (English)

    Ding Xiang; Rong Xiaofeng; Deng Yan; Yu Xinglong

    2006-01-01

    High resolution of surface plasmon resonance (SPR) detection is of vital importance. SPR biosensing system resolution is determined by intrinsic sensitivity of biochip and light signal acquisition system. In this article, different signal acquisition system resolutions on photodetector were analyzed based on light intensity and phase detection. Result shows that charge coupled device (CCD) with larger numbers of pixels is potential to achieve higher detection resolution. A 64 pixel line array CCD and a 12 bit ADC can achieve resolution of 10-7 refractive index unit (RIU). In array detection mode, increasing of detection throughput is at the cost of decreasing system resolution. Simulation analysis indicates that, if noise is taken into account, phase modulation methods are capable of providing better noise reduction performance than intensity methods.

  12. A device design of an integrated CMOS poly-silicon biosensor-on-chip to enhance performance of biomolecular analytes in serum samples.

    Science.gov (United States)

    Pei-Wen, Yen; Che-Wei, Huang; Yu-Jie, Huang; Min-Cheng, Chen; Hsin-Hao, Liao; Shey-Shi, Lu; Chih-Ting, Lin

    2014-11-15

    For on-site clinical diagnosis of biomolecules, the detection performances of most point-of-care (POC) biosensor devices are limited by undesired cross-detection of other non-analyte proteins in patient serum samples and other complex samples. To conquer this obstacle, this work presents a fully integrated bottom-gate poly-silcion nanowire (polySi NW) biosensor system-on-chip (SoC) to enhance the detection performance of cardiac-specific troponin-I (cTnI) concentration levels in serum samples. By applying proper electrical potential at the bottom gate under polySi NW biosensor, the biosensor response to cTnI biomarker can be improved by at least 16 fold in 50% phantom serum samples. The experimental result shows its detection range is from 3.2 × 10(-13)M(mol l(-1)) to 3.2 × 10(-10)M. This enhancement can be attributed to the electrostatic interactions between target biomolecules and voltage-applied bottom gate electrodes. This is the first time that a polySi NW CMOS biosensor chip has shown feasibilities to detect specific biomarkers in serum samples. Therefore, the developed technology paves the way toward on-field applications of CMOS compatible SiNW biosensing technologies and it can be employed for future biomolecular analysis in on-site serum diagnosis applications.

  13. GNSS-based Road Charging Systems - Assessment of Vehicle Location Determination

    DEFF Research Database (Denmark)

    Zabic, Martina

    , it is important to highlight the overall system architecture and define the essential system functions and describe the relationship among them. The framework is used as a means to structure the discussion about the technological challenges of GNSS-based road charging systems. The thesis discusses the overall...... charging systems. The technical experiment conducted in this PhD study proved to suffer from different technical challenges which had different impacts on the overall system dependability. Due to these challenges, data includes both inaccurate and incomplete data information, and it is hence concluded......). The research presented in this thesis deals with the performance and technological challenges of vehicle location determination within GNSS-based road charging systems. GNSS-based road charging systems may take on a number of different forms. Depending on the charging objective, these road charging systems can...

  14. Social determinants of health inequalities: towards a theoretical perspective using systems science.

    Science.gov (United States)

    Jayasinghe, Saroj

    2015-08-25

    A systems approach offers a novel conceptualization to natural and social systems. In recent years, this has led to perceiving population health outcomes as an emergent property of a dynamic and open, complex adaptive system. The current paper explores these themes further and applies the principles of systems approach and complexity science (i.e. systems science) to conceptualize social determinants of health inequalities. The conceptualization can be done in two steps: viewing health inequalities from a systems approach and extending it to include complexity science. Systems approach views health inequalities as patterns within the larger rubric of other facets of the human condition, such as educational outcomes and economic development. This anlysis requires more sophisticated models such as systems dynamic models. An extension of the approach is to view systems as complex adaptive systems, i.e. systems that are 'open' and adapt to the environment. They consist of dynamic adapting subsystems that exhibit non-linear interactions, while being 'open' to a similarly dynamic environment of interconnected systems. They exhibit emergent properties that cannot be estimated with precision by using the known interactions among its components (such as economic development, political freedom, health system, culture etc.). Different combinations of the same bundle of factors or determinants give rise to similar patterns or outcomes (i.e. property of convergence), and minor variations in the initial condition could give rise to widely divergent outcomes. Novel approaches using computer simulation models (e.g. agent-based models) would shed light on possible mechanisms as to how factors or determinants interact and lead to emergent patterns of health inequalities of populations.

  15. Quantum algorithms and mathematical formulations of biomolecular solutions of the vertex cover problem in the finite-dimensional hilbert space.

    Science.gov (United States)

    Chang, Weng-Long; Ren, Ting-Ting; Feng, Mang

    2015-01-01

    In this paper, it is shown that the proposed quantum algorithm for implementing Boolean circuits generated from the DNA-based algorithm solving the vertex-cover problem of any graph G with m edges and n vertices is the optimal quantum algorithm. Next, it is also demonstrated that mathematical solutions of the same biomolecular solutions are represented in terms of a unit vector in the finite-dimensional Hilbert space. Furthermore, for testing our theory, a nuclear magnetic resonance (NMR) experiment of three quantum bits to solve the simplest vertex-cover problem is completed.

  16. A Theoretical Study of Distribution of First Passage Times of Biomolecular Folding and Reactions with Application to Single Molecules

    Science.gov (United States)

    Wang, Jin; Leite, Vitor; Stell, George; Lee, Chi-Lun

    2002-03-01

    We study the distribution of first passage times of biomolecular folding and reactions through the general framework of energy landscape theory. Both the analytical and lattice simulation results show above cirtain specific temperature, the distribution of first passage time is log-normal, while under the same temperature, the distribution starts to develop fatty tails and deviate from the log-normal distribution, indicating intermittency whereas rare events might dominate the whole process. A power law distribution of first passage time was found analytically in this situation. Applications and connections to experiments on single molecule reaction dynamics are studied.

  17. A concept of a component based system to determine pot-plant shelf-life

    DEFF Research Database (Denmark)

    Körner, Oliver; Skou, Anne-Marie Thonning; Aaslyng, Jesper Peter Mazanti;

    2006-01-01

    to calculate the expected keeping quality, or it will be able to apply the system as decision support during plant cultivation. In the latter case, the model-based system can be implemented in a greenhouse climate computer. The concept contains information on climate control strategies, controlled stress......, the keeping quality of a plant after removal from the greenhouse could be estimated. A concept of a system that describes a model based knowledge system aiming at determination of the last selling date for pot plants is presented. The core of the conceptual system is a tool that can either be used......Plant keeping quality during shelf life is next to genetic attributes also determined by plant treatment. This is attributed to inner plant quality parameters. We expect that a model including information gathered during crop cultivation could be used to predict the inner crop quality. From that...

  18. Determination of continuous system transfer functions from sampled pulse response data

    Science.gov (United States)

    Jordan, Jay B.; Watkins, Wendell R.; Palacios, Fernando R.; Billingsley, Daniel R.

    1994-12-01

    A method for determining the transfer function of a continuous system from sampled responses to single- and multiple-pulse excitation is presented. The method is an extension of the sampled-edge-response method pioneered by the theoretical work of A. Papoulis in 1962 and the application of the theory to optical systems by B. Tatian in 1965. Occasions arise when pulse rather than step-function stimuli are available for system excitations. In such cases, the method presented is useful for determining the system transfer function. The use of antialiasing filters and estimation of non-bandwidth-limited transfer functions are discussed. Practical application of the method to characterizing the system transfer function of a commercial 8- to 12-micrometers infrared imager is also presented.

  19. Determination of solute organic concentration in contaminated soils using a chemical-equilibrium soil column system

    DEFF Research Database (Denmark)

    Gamst, Jesper; Kjeldsen, Peter; Christensen, Thomas Højlund

    2007-01-01

    Groundwater risk assessment of contaminated soils implies determination of the solute concentration leaching out of the soil. Determination based on estimation techniques or simple experimental batch approach has proven inadequate. Two chemical equilibrium soil column leaching tests...... for determination of solute concentration in a contaminated soil were developed; (1) a chemical Equilibrium and Recirculation column test for Volatile organic chemicals (ER-V) and (2) a chemical Equilibrium and Recirculation column test for Hydrophobic organic chemicals (ER-H). The two test systems were evaluated...... to measure solute phase concentration of PAHs in contaminated soils. Overall a reliable and reproducable system for determining solute concentration of a wide range of organic compounds in contaminated soils has been developed....

  20. An error criterion for determining sampling rates in closed-loop control systems

    Science.gov (United States)

    Brecher, S. M.

    1972-01-01

    The determination of an error criterion which will give a sampling rate for adequate performance of linear, time-invariant closed-loop, discrete-data control systems was studied. The proper modelling of the closed-loop control system for characterization of the error behavior, and the determination of an absolute error definition for performance of the two commonly used holding devices are discussed. The definition of an adequate relative error criterion as a function of the sampling rate and the parameters characterizing the system is established along with the determination of sampling rates. The validity of the expressions for the sampling interval was confirmed by computer simulations. Their application solves the problem of making a first choice in the selection of sampling rates.

  1. Determinants of Performance of Health Systems Concerning Maternal and Child Health: A Global Approach

    OpenAIRE

    2015-01-01

    Aims To assess the association of social determinants on the performance of health systems around the world. Methods A transnational ecological study was conducted with an observation level focused on the country. In order to research on the strength of the association between the annual maternal and child mortality in 154 countries and social determinants: corruption, democratization, income inequality and cultural fragmentation, we used a mixed linear regression model for repeated measures ...

  2. METHOD FOR IN SITU DETERMINATION OF PCO2 IN SEA-AIR EQUILIBRIUM SYSTEM

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The method for determining PCO2 in the atmosphere and water by using gas chromatography was studied. For determination of PCO2 in the atmosphere, a sampling method was developed in which the chromatograph was connected to a 6-port valve with a sampling pipe opening to the atmosphere, so gas pressure in the sampling pipe was identical to that of the atmosphere. A semi-automatic seawater-atmosphere equilibrium system was designed to determine the PCO2 in seawater. The equilibrium chamber contained in situ seawater and the well-equilibrated gas was pushed into the sampling pipe by sample water, so pressure and temperature calibration could be avoided. This method has high accuracy for the determination of PCO2 in the air and seawater, and was used for in situ determination of PCO2 in the atmosphere and of the seawater sample in the JGOFS cruise in the East China Sea.

  3. METHOD FOR IN SITU DETERMINATION OF Pco2 IN SEA-AIR EQUILIBRIUM SYSTEM

    Institute of Scientific and Technical Information of China (English)

    崔鹤; 纪雷; 王军; 辛淑平; 张龙军; 陆贤昆

    2001-01-01

    The method for determining Pco2 in the atmosphere and water by using gas chroma-tography was studied. For determination of Pco2 in the atmosphere, a sampling method was developed in which the chromatograph was connected to a 6-port valve with a sampling pipe opening to the atmosphere, so gas pressure in the sampling pipe was identical to that of the atmoesphere. A semi-automatic seawater-atmosphere equilibrium system was designed to determine the Pco2 in seawater. The equilibrium chamber contained in situ seawater and the well-equilibrated gas was pushed into the sampling pipe by sample wa-ter, so pressure and temperature calibration could be avoided. This method has high accuracy for the de-termination of Pco2 in the air and seawater, and was used for in situ determination of Pco2 in the atmo-sphere and of the seawater sample in the JGOFS cruise in the East China Sea.

  4. A System Analysis for Determining Alternative Technological Issues for the Future

    Science.gov (United States)

    Magistrale, V. J.; Small, J.

    1967-01-01

    A systems engineering methodology is provided, by which future technological ventures may be examined utilizing particular national, corporate, or individual value judgments. Three matrix analyses are presented. The first matrix is concerned with the effect of technology on population increase, war, poverty, health, resources, and prejudice. The second matrix explores an analytical technique for determining the relative importance of different areas of technology. The third matrix explores how an individual or corporate entity may determine how its capability may be used for future technological opportunities. No conclusions are presented since primary effort has been placed on the methodology of determining future technological issues.

  5. A STUDY ON DETERMINING THE REFERENCE SPREADING SEQUENCES FOR A DS/CDMACOMMUNICATION SYSTEM

    Directory of Open Access Journals (Sweden)

    Cebrail ÇİFTLİKLİ

    2002-02-01

    Full Text Available In a direct sequence/code division multiple access (DS/CDMA system, the role of the spreading sequences (codes is crucial since the multiple access interference (MAI is the main performance limitation. In this study, we propose an accurate criterion which enables the determination of the reference spreading codes which yield lower bit error rates (BER's in a given code set for a DS/CDMA system using despreading sequences weighted by stepping chip waveforms. The numerical results show that the spreading codes determined by the proposed criterion are the most suitable codes for using as references.

  6. On the possibility of determining anthracycline antibiotics in aqueous solutions using optical analytical system (biosensor)

    Science.gov (United States)

    Yevdokimov, Yu. M.; Skuridin, S. G.; Salyanov, V. I.; Semenov, S. V.; Sol'ev, P. N.; Valuev-Elliston, V. T.; Vereshchagin, F. V.; Chulkov, D. P.; Kompanets, O. N.

    2017-02-01

    We propose a version of the theory describing the circular dichroism spectra of cholesteric liquidcrystal dispersion particles of double-stranded DNA. The basis of the theory is the concept of absorption of electromagnetic waves by large molecular systems. The effect of physical parameters of dispersion particles on their circular dichroism is theoretically determined. It is experimentally demonstrated that circular dichroism can be used as a convenient tool for creating an optical analytical system for the determination of biologically active compounds that interact with DNA molecules.

  7. Determination of contact parameters for discrete element method simulations of granular systems

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Both linear-spring-dashpot (LSD) and non-linear Hertzian-spring-dnshpot (HSD) contact models are commonly used for the calculation of contact forces in Discrete Element Method (DEM) simulations of granular systems.Despite the popularity of these models, determination of suitable values for the contact parameters of the simulated particles such as stiffness, damping coefficient, coefficient of restitution, and simulation time step,is not altogether obvious.In this work the relationships between these contact parameters for a model system where a particle impacts on a flat base are examined.Recommendations are made concerning the determination of these contact parameters for use in DEM simulations.

  8. Performance analysis of an integrated GPS/inertial attitude determination system. M.S. Thesis - MIT

    Science.gov (United States)

    Sullivan, Wendy I.

    1994-01-01

    The performance of an integrated GPS/inertial attitude determination system is investigated using a linear covariance analysis. The principles of GPS interferometry are reviewed, and the major error sources of both interferometers and gyroscopes are discussed and modeled. A new figure of merit, attitude dilution of precision (ADOP), is defined for two possible GPS attitude determination methods, namely single difference and double difference interferometry. Based on this figure of merit, a satellite selection scheme is proposed. The performance of the integrated GPS/inertial attitude determination system is determined using a linear covariance analysis. Based on this analysis, it is concluded that the baseline errors (i.e., knowledge of the GPS interferometer baseline relative to the vehicle coordinate system) are the limiting factor in system performance. By reducing baseline errors, it should be possible to use lower quality gyroscopes without significantly reducing performance. For the cases considered, single difference interferometry is only marginally better than double difference interferometry. Finally, the performance of the system is found to be relatively insensitive to the satellite selection technique.

  9. System and method for determining stator winding resistance in an AC motor using motor drives

    Science.gov (United States)

    Lu, Bin; Habetler, Thomas G; Zhang, Pinjia

    2013-02-26

    A system and method for determining the stator winding resistance of AC motors is provided. The system includes an AC motor drive having an input connectable to an AC source and an output connectable to an input terminal of an AC motor, a pulse width modulation (PWM) converter having switches therein to control current flow and terminal voltages in the AC motor, and a control system connected to the PWM converter. The control system generates a command signal to cause the PWM converter to control an output of the AC motor drive corresponding to an input to the AC motor, selectively generates a modified command signal to cause the PWM converter to inject a DC signal into the output of the AC motor drive, and determines a stator winding resistance of the AC motor based on the DC signal of at least one of the voltage and current.

  10. System and method for determining stator winding resistance in an AC motor

    Science.gov (United States)

    Lu, Bin; Habetler, Thomas G.; Zhang, Pinjia; Theisen, Peter J.

    2011-05-31

    A system and method for determining stator winding resistance in an AC motor is disclosed. The system includes a circuit having an input connectable to an AC source and an output connectable to an input terminal of an AC motor. The circuit includes at least one contactor and at least one switch to control current flow and terminal voltages in the AC motor. The system also includes a controller connected to the circuit and configured to modify a switching time of the at least one switch to create a DC component in an output of the system corresponding to an input to the AC motor and determine a stator winding resistance of the AC motor based on the injected DC component of the voltage and current.

  11. Determination of characteristics of feromagnetic material using modern data acquisition system

    Directory of Open Access Journals (Sweden)

    Koprivica Branko

    2009-01-01

    Full Text Available This paper describes the use of modern measuring and data acquisition system for determining characteristics of feromagnetic material. For this purpose data acquisition card NI USB-6009, PC with data acquisition software and fluxmeter Electrical Steel Measuring System MPG 100 D were used. Based on the results obtained by measurements the modeling of hysteresis loop is performed by using appropriate mathematical model.

  12. General criteria for determining rotation or oscillation in a two-dimensional axisymmetric system

    Science.gov (United States)

    Koyano, Yuki; Yoshinaga, Natsuhiko; Kitahata, Hiroyuki

    2015-07-01

    A self-propelled particle in a two-dimensional axisymmetric system, such as a particle in a central force field or confined in a circular region, may show rotational or oscillatory motion. These motions do not require asymmetry of the particle or the boundary, but arise through spontaneous symmetry breaking. We propose a generic model for a self-propelled particle in a two-dimensional axisymmetric system. A weakly nonlinear analysis establishes criteria for determining rotational or oscillatory motion.

  13. The determination of the reference system of a single observer observed quantities

    Energy Technology Data Exchange (ETDEWEB)

    Epikhin, E.N.

    1979-01-01

    The paper examines various methods for constructing single-observer reference systems in general relativity. The procedure involves the determination on Riemann space of: (1) the world line of the observer, (2) the lines of transfer, and (3) a method for transferring quantities to the world line of the observer. Particular attention is given to the gauge transformation of synchronized single-observer reference systems. The examination is performed in a monad-field framework.

  14. Determination of Dead Time of Neutron Counting System for Use of Reactor Start up

    Institute of Scientific and Technical Information of China (English)

    ZHAOYu-sen; ZHAOPeng-yu

    2003-01-01

    The dead time is important parameter of neutron counting system for use of reactor start up. It is relative to accurate determination of critical mass and the safety during reactor start up. So, it is important that dear time is measured accurately. There are many methods for measuring the dead time, but they are rare to be suitable for neutron counting system, which has wide variant range.

  15. New product development with the innovative biomolecular sublingual immunotherapy formulations for the management of allergic rhinitis

    Directory of Open Access Journals (Sweden)

    Frati F

    2014-09-01

    Full Text Available Franco Frati,1 Lorenzo Cecchi,2,3 Enrico Scala,4 Erminia Ridolo,5 Ilaria Dell'Albani,1 Eleni Makrì,6 Giovanni Pajno,7 Cristoforo Incorvaia6 1Medical and Scientific Department, Stallergenes, Milan, Italy; 2Interdepartmental Centre of Bioclimatology, University of Florence, Florence, Italy; 3Allergy and Clinical Immunology Section, Azienda Sanitaria di Prato, Prato, Italy; 4Experimental Allergy Unit, IDI-IRCCS, Rome, Italy; 5Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy; 6Allergy/Pulmonary Rehabilitation, ICP Hospital, Milan, Italy; 7Department of Pediatrics, Allergy Unit, University of Messina, Messina, Italy Abstract: The molecular allergy technique, currently defined as component-resolved diagnosis, significantly improved the diagnosis of allergy, allowing for differentiation between molecules actually responsible for clinical symptoms (genuine sensitizers and those simply cross-reacting or shared by several sources (panallergens, thus influencing the appropriate management of a patient's allergy. This also concerns allergen immunotherapy (AIT, which may be prescribed more precisely based on the component-resolved diagnosis results. However, the advance in diagnosis needs to be mirrored in AIT. According to consensus documents and to expectations of specialists, therapy should be based on standardized extracts containing measured amounts of the clinically relevant molecules, ie, the major allergens. The new generation of extracts for sublingual immunotherapy fulfills these requirements and are thus defined as biomolecular (BM. BM refers to natural extracts with a defined content of major allergens in micrograms. All Staloral BM products are indicated for the treatment of allergic rhinitis with or without asthma. The effectiveness of AIT is related to its ability to modify the immunological response of allergic subjects. The 5-grass and house dust mite extracts were evaluated addressing the T helper 1, T

  16. Synthesis and biosynthesis of {sup 13}C-, {sup 15}N-labeled deoxynucleosides useful for biomolecular structural determinations

    Energy Technology Data Exchange (ETDEWEB)

    Ashburn, D.A.; Garcia, K.; Hanners, J.L.; Silks, L.A. III; Unkefer, C.J. [Los Alamos National Laboratory, NM (United States)

    1994-12-01

    Currently, there is a great emphasis on elucidating the structure, function, and dynamics of DNA. Much of the research involved in this study uses nuclear magnetic resonance (NMR) spectroscopy. Effective use of NMR spectroscopy for DNA molecules with mw > 10,000 requires stable isotope enrichment. We present strategies for site-specific isotopic labeling of the purine bases adenosine and guanosine and the biosynthesis of (U-{sup 13}C, {sup 15}N) DNA from methylotropic bacteria. With commercially available 6-chloropurine, an effective two-step route leads to 2{prime}-deoxy-(amino-{sup 15}N)adenosine (dA). The resulting d(amino-{sup 15}N)A is used in a series of reactions to synthesize 2{prime}-deoxy-(2-{sup 13}C,1,amino-{sup 15}N{sub 2})guanosine or any combination thereof. An improved biosynthesis of labeled DNA has been accomplished using Methylobacterium extorquens AS1. Each liter of growth medium contains 4 g of methanol to yield 1 g of lyophilized cells. As much as 200 mg of RNA per liter of culture has been obtained. We are currently developing large-scale isolation protocols. General synthetic pathways to oligomeric DNA will be presented.

  17. Pushing back the frontiers of mercury speciation using a combination of biomolecular and isotopic signatures: challenge and perspectives.

    Science.gov (United States)

    Pedrero, Zoyne; Donard, Olivier F X; Amouroux, David

    2016-04-01

    Mercury (Hg) pollution is considered a major environmental problem due to the extreme toxicity of Hg. However, Hg metabolic pathways in biota remain elusive. An understanding of these pathways is crucial to elucidating the (eco)toxic effects of Hg and its biogeochemical cycle. The development of a new analytical methodology based on both speciation and natural isotopic fractionation represents a promising approach for metabolic studies of Hg and other metal(loid)s. Speciation provides valuable information about the reactivity and potential toxicity of metabolites, while the use of natural isotopic signature analysis adds a complementary dynamic dimension that allows the life history of the target element to be probed, the source of the target element (i.e., the source of pollution) to be identified, and reactions to be tracked. The resulting combined (bio)molecular and isotopic signature affords precious insight into the behavior of Hg in biota and Hg detoxification mechanisms. In the long term, this highly innovative methodology could be used in life and environmental science studies of metal(loid)s to push back the frontiers of our knowledge in this field. This paper summarizes the current status of the application of Hg speciation and the isotopic signature of Hg at the biomolecular level in living organisms, and discusses potential future uses of this combination of techniques.

  18. Unraveling the biomolecular snapshots of mitosis in healthy and cancer cells using plasmonically-enhanced Raman spectroscopy.

    Science.gov (United States)

    Panikkanvalappil, Sajanlal R; Hira, Steven M; Mahmoud, Mahmoud A; El-Sayed, Mostafa A

    2014-11-12

    Owing to the dynamic and complex nature of mitosis, precise and timely executions of biomolecular events are critical for high fidelity cell division. In this context, visualization of such complex events at the molecular level can provide vital information on the biomolecular processes in abnormal cells. Here, we explored the plasmonically enhanced light scattering properties of functionalized gold nanocubes (AuNCs) together with surface-enhanced Raman spectroscopy (SERS) to unravel the complex and dynamic biological processes involved in mitosis of healthy and cancerous cells from its molecular perspectives. By monitoring various stages of mitosis using SERS, we noticed that relatively high rate of conversion of mitotic proteins from their α-helix structure to β-sheet conformation is likely in the cancer cells during meta-, ana-, and telophases. Unique biochemical modifications to the lipid and amino acid moieties, associated with the observed protein conformational modifications, were also identified. However, in healthy cells, the existence of proteins in their β conformation was momentary and was largely in the α-helix form. The role of abnormal conformational modifications of mitotic proteins on the development of anomalous mitotic activities was further confirmed by looking at plasmonic nanoparticle-induced cytokinesis failure in cancer cells. Our findings illustrate the vast possibilities of SERS in real-time tracking of complex, subtle, and momentary modifications of biomolecules in live cells, which could provide new insights to the role of protein conformation dynamics during mitosis on the development of cancer and many other diseases.

  19. Heuristic Optimization Techniques for Determining Optimal Reserve Structure of Power Generating Systems

    DEFF Research Database (Denmark)

    Ding, Yi; Goel, Lalit; Wang, Peng

    2012-01-01

    cost of the system will also increase. The reserve structure of a MSS should be determined based on striking a balance between the required reliability and the reserve cost. The objective of reserve management for a MSS is to schedule the reserve at the minimum system reserve cost while maintaining......Electric power generating systems are typical examples of multi-state systems (MSS). Sufficient reserve is critically important for maintaining generating system reliabilities. The reliability of a system can be increased by increasing the reserve capacity, noting that at the same time the reserve...... the required level of supply reliability to its customers. In previous research, Genetic Algorithm (GA) has been used to solve most reliability optimization problems. However, the GA is not very computationally efficient in some cases. In this chapter a new heuristic optimization technique—the particle swarm...

  20. Probing the interplay between factors determining reaction rates on silica gel using termolecular systems.

    Science.gov (United States)

    Kirkpatrick, Iain; Worrall, David R; Williams, Siân L; Buck, Craig J T; Meseguer, Rafael G

    2012-10-01

    In this study we have compared energy and electron transfer reactions in termolecular systems using a nanosecond diffuse reflectance laser flash photolysis technique. We have previously investigated these processes on silica gel surfaces for bimolecular systems and electron transfer in termolecular systems. The latter systems involved electron transfer between three arene molecules with azulene acting as a molecular shuttle. In this study we present an alternative electron transfer system using trans β-carotene as an electron donor in order to effectively immobilise all species except the shuttle, providing the first unambiguous evidence for radical ion mobility. In the energy transfer system we use naphthalene, a structural isomer of azulene, as the shuttle, facilitating energy transfer from a selectively excited benzophenone sensitiser to 9-cyanoanthracene. Bimolecular rate constants for all of these processes have been measured and new insights into the factors determining the rates of these reactions on silica gel have been obtained.

  1. Determining the number of kanbans for dynamic production systems: An integrated methodology

    Directory of Open Access Journals (Sweden)

    Özlem Uzun Araz

    2016-08-01

    Full Text Available Just-in-time (JIT is a management philosophy that reduces the inventory levels and eliminates manufacturing wastes by producing only the right quantity at the right time. A kanban system is one of the key elements of JIT philosophy. Kanbans are used to authorize production and to control movement of materials in JIT systems. In Kanban systems, the efficiency of the manufacturing system depends on several factors such as number of kanbans, container size etc. Hence, determining the number of kanbans is a critical decision in Kanban systems. The aim of this study is to develop a methodology that can be used in order to determine the number of kanbans in a dynamic production environment. In this methodology, the changes in system state is monitored in real time manner, and the number of the kanbans are dynamically re-arranged. The proposed methodology integrates simulation, neural networks and Mamdani type fuzzy inference system. The methodology is modelled in simulation environment and applied on a hypothetic production system. We also performed several comparisons for different control policies to show the effectiveness of the proposed methodology.

  2. Teaching and Learning the Interplay between Chance and Determinism in Nonlinear Systems

    Science.gov (United States)

    Stavrou, Dimitrios; Duit, Reinders

    2014-01-01

    That the interplay of random and deterministic processes may result in both the limited predictability of nonlinear systems and the formation of structures seems to be a most valuable general insight into the nature of science. This study investigates the possibility of teaching and learning the interplay of chance and determinism in nonlinear…

  3. Generation and use of the Goddard trajectory determination system SLP ephemeris files

    Science.gov (United States)

    Armstrong, M. G.; Tomaszewski, I. B.

    1973-01-01

    Information is presented to acquaint users of the Goddard Trajectory Determination System Solar/Lunar/Planetary ephemeris files with the details connected with the generation and use of these files. In particular, certain sections constitute a user's manual for the ephemeris files.

  4. A model for determining condition-based maintenance policies for deteriorating multi-component systems

    NARCIS (Netherlands)

    Hontelez, J.A.M.; Wijnmalen, D.J.D.

    1993-01-01

    We discuss a method to determine strategies for preventive maintenance of systems consisting of gradually deteriorating components. A model has been developed to compute not only the range of conditions inducing a repair action, but also inspection moments based on the last known condition value so

  5. Flow injection chemiluminescence determination of loxoprofen and naproxen with the acidic permanganate-sulfite system

    Institute of Scientific and Technical Information of China (English)

    Li-Juan Wang; Yu-Hai Tang; Yang-Hao Liu

    2011-01-01

    A novel flow injection chemiluminescence(CL)method for the determination of loxoprofen and naproxen was proposed based on the CL system of KMnO4 and Na2SO3 in acid media.The CL intensity of KMnO4-Na2SO3 was greatly enhanced in the presence of loxoprofen a

  6. Using Determinants and Computers to Recognize Dependent and Inconsistent Linear Systems.

    Science.gov (United States)

    Conklin, Kenneth R.

    1981-01-01

    A computer program that uses determinants to solve simultaneous systems of equations is presented. The purpose is to show teachers how to use topics from algebra, geometry, and programing to lead pupils to appreciate the beauty and unity of mathematics. (MP)

  7. Validation of the FACSCount AF system for determination of sperm concentration in boar semen

    DEFF Research Database (Denmark)

    Hansen, C.; Christensen, P.; Stryhn, H.

    2002-01-01

    A flow cytometric method has been developed for rapid determination of sperm concentration in semen from various mammalian species.* All cells containing DNA are stained with SYBR-14 or propidium iodide (PI) and sperm concentration is determined in relation to an internal standard of fluorescent...... microspheres ( beads). Satisfactory staining can be achieved within 2-3 min and the following flow cytometric analysis on the FACSCount AF System rapidly provides the user with a precise and accurate assessment of the sperm concentration. In this study, the FACSCount AF System and Sperm Counting Reagent ( BD...... Biosciences) was compared with microscopic counting using a Burker-Turk haemocytometer. In addition, sperm concentration was determined using the Corning 254 spectrophotometer which is used routinely by Danish artificial insemination stations for boars. The results show that the agreement between flow...

  8. Application of Nuclear Magnetic Resonance and Hybrid Methods to Structure Determination of Complex Systems.

    Science.gov (United States)

    Prischi, Filippo; Pastore, Annalisa

    2016-01-01

    The current main challenge of Structural Biology is to undertake the structure determination of increasingly complex systems in the attempt to better understand their biological function. As systems become more challenging, however, there is an increasing demand for the parallel use of more than one independent technique to allow pushing the frontiers of structure determination and, at the same time, obtaining independent structural validation. The combination of different Structural Biology methods has been named hybrid approaches. The aim of this review is to critically discuss the most recent examples and new developments that have allowed structure determination or experimentally-based modelling of various molecular complexes selecting them among those that combine the use of nuclear magnetic resonance and small angle scattering techniques. We provide a selective but focused account of some of the most exciting recent approaches and discuss their possible further developments.

  9. Eddy current measurement system evaluation for corrosion depth determination on cast aluminum aircraft structure

    Science.gov (United States)

    Singh, Surendra; Greving, Dan; Kinney, Andy; Vensel, Fred; Ohm, Jim; Peeler, Mike

    2013-01-01

    An eddy current (EC) technique was developed to determine the corrosion depth on a bare flange face of a cast aluminum A356-T6 aircraft engine structure. The EC response and the corrosion depths determined through metallurgical cross sections were used to develop an empirical relation between EC response and depth. The EC technique and depth determination are used to inspect the engine structures during overhaul to determine if they are fit for continued service. An accurate and reliable Non-Destructive Inspection is required to ensure that structures returned to service are safe for continued operation. NDE system reliability demonstrations of the eddy current technique are traditionally reported in terms of Probability of Detection (POD) data using MIL-HDBK-1823A. However, the calculation of POD data is based on a simple linear predictive model that is valid only if certain criteria are met. These are: 1) NDE system response is measurable (i.e. continuous data), 2) Flaw size is known and measurable (i.e. continuous data), 3) relationship between the NDE system response and flaw size is linear (or linear on a log scale), 4) variation in measured responseresponse around a predicted response for a given flaw size is normally distributed, 5) the variation around the predicted response is constant (i.e. variation does not change with flaw size), and 6) inherent variability in the NDE system is known and fully understood. In this work, a Measurement System Evaluation (MSE) of the Eddy Current System was used to address some of these concerns. This work was completed on two aircraft structures having varying corrosion depths. The data were acquired in a random manner at fifty regions of interests (ROIs). Three operators participated in this study, and each operator measured Eddy Current response three times in each ROI. In total, there were four hundred and fifty data points collected. Following this, the two structures were sectioned for measuring corrosion depth. The

  10. Determination of Critical Parameters of Carbon Dioxide+ Butyraldehyde System with Different Compositions

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jing-chang; GAO Xi-xin; CAO Wei-liang

    2005-01-01

    Supercritical carbon dioxide( SC-CO2 ) is considered in green chemistry as a substitute for conventional solvents in chemical reactions due to its environmentally benign character. Recently we have reported the homogeneous hydroformylation of propylene in supercritical carbon dioxide( SC-CO2 ), which is an example of this kind of application of carbon dioxide. The determination for the critical parameters of carbon dioxide + butyraldehyde mixtures is necessary for this reaction design which is the focus of the present paper. The critical parameters of the binary systems were determined via the static visual method at a constant volume with the molar fraction of butyraldehyde ranging from 1.0%to 2. 2% and the pressure ranging from 5 to 10 MPa. The experimental results show that the critical pressure and temperature increased with increasing the molar fraction of butyraldehyde. The bubble(dew) temperatures and the bubble (dew) pressures for the binary systems were also determined experimentally. The p-T Figures at different compositions of the binary systems were described. In addition, the critical compressibility factors Zc of the binary systems at different concentrations of n-butyraldehyde were calculated. It was found that the critical compressibility factor values of the binary systems decreased with increasing the molar fraction of n-butyraldehyde in the experimental range.

  11. Methodology and key determinants of building an efficient national innovation system of a country

    Directory of Open Access Journals (Sweden)

    Viktoriia Gurova

    2015-12-01

    Full Text Available The paper represents a research of theoretical principles for determining national innovation systems, as well as analyzes performance results displayed by national innovation systems of the leading countries in the global innovation space, while also describing characteristic features thereof and formulating recommendations for NIS build-up based on the same, implementation of which should serve as the basis of the national innovation system effective performance. It has been determined that at the current stage of global economy development such factors as science, technology and innovation play an important role in formation of a competitive economy. It has been established that the overall funding level with respect to science proves one of the key characteristics of an innovative country, and therefore NIS performance analysis was carried out based on the national expenditure indicator regarding research and development as well as on the country's position in the Global Innovation Index. The analysis carried out showed that the NISs of certain countries were more efficient than those of the others due to peculiarities of the innovative system elements that can be further referred to as determinants of building an effective national innovation system of a country

  12. Real-time Imaging Orientation Determination System to Verify Imaging Polarization Navigation Algorithm

    Directory of Open Access Journals (Sweden)

    Hao Lu

    2016-01-01

    Full Text Available Bio-inspired imaging polarization navigation which can provide navigation information and is capable of sensing polarization information has advantages of high-precision and anti-interference over polarization navigation sensors that use photodiodes. Although all types of imaging polarimeters exist, they may not qualify for the research on the imaging polarization navigation algorithm. To verify the algorithm, a real-time imaging orientation determination system was designed and implemented. Essential calibration procedures for the type of system that contained camera parameter calibration and the inconsistency of complementary metal oxide semiconductor calibration were discussed, designed, and implemented. Calibration results were used to undistort and rectify the multi-camera system. An orientation determination experiment was conducted. The results indicated that the system could acquire and compute the polarized skylight images throughout the calibrations and resolve orientation by the algorithm to verify in real-time. An orientation determination algorithm based on image processing was tested on the system. The performance and properties of the algorithm were evaluated. The rate of the algorithm was over 1 Hz, the error was over 0.313°, and the population standard deviation was 0.148° without any data filter.

  13. Application of flow-injection potentiometric system for determination of total concentration of aliphatic carboxylic acids.

    Science.gov (United States)

    Mroczkiewicz, Monika; Górski, Łukasz; Zamojska-Jaroszewicz, Anna; Szewczyk, Krzysztof W; Malinowska, Elżbieta

    2011-09-30

    In this work, flow-injection system with potentiometric detection was tested for determination of total carboxylic acid concentration. Detection part of the examined system consists of ion-selective electrodes (ISEs) with polymer membranes of different compositions. First electrode is based on Zr(IV)-tetraphenylporphyrin as ionophore selective towards carboxylic acid anions, the membrane of second one contains only liphophilic anion exchanger - tridodecylmethylammonium chloride. Final response of the system is a result of combination of EMF signals from both electrodes. Combination of two detectors enables significant decrease of differences between potentiometric signals induced by mixtures of studied anions of various concentrations as compared to results obtained only with metalloporphyrin-based ISE. The use of anion-exchanger based detector allows for elimination of the influence of aliphatic carboxylic acids lipophilicity. Proposed potentiometric flow-injection system was employed for determination of short-chain aliphatic carboxylic acids (so-called VFA - volatile fatty acids) in samples originating from an anaerobic digester. Results obtained for these relatively complicated samples are in good agreement with results obtained with the use of reference colorimetric method. Linear response towards carboxylic acids was observed in the concentration range of 10(-4) to 10(-2)mold m(-3), with the slopes in the range of -110 to -150 mV dec(-1) (for acetate(-) and butyrate(-), respectively). System enables for determination of about 6 samples per hour. Life time of ISEs average about 2 months.

  14. Determination of important pipes segments in water distribution systems using the hydraulic vulnerability

    Directory of Open Access Journals (Sweden)

    Bruno Segalla Pizzolatti

    2008-12-01

    Full Text Available Water supply systems, due to their configuration, tend to be vulnerable to internal and external threats, which can potentially cause instability in water distribution. The vulnerability assessment is a tool that has been used to ensure the water supply in different failure scenarios, and can assist in seeking alternatives for supplying water in emergency situations. This work aimed mainly at determining the most important or critical segments for an adequate performance of the water supply system when there are emergency conditions such as the ones caused by natural disasters. The system’s hydraulic performance was evaluated based on simulations using EPANET 2.0. The vulnerability was determined by using an application written in Visual Basic 6.0 to customize EPANET using its Programmer's Toolkit. The system vulnerability was determined with the interruption of one segment at a time to calculate, in a dynamic way, the importance of each segment to the system, and by comparison of these results to the index of relative importance by flow rate. The results showed that using the indices Vulnerability-System and Vulnerability-Node was adequate to establish the importance of a critical segment in the performance of a network.

  15. An inclined plane system with microcontroller to determine limb motor function of laboratory animals.

    Science.gov (United States)

    Chang, Ming-Wen; Young, Ming-Shing; Lin, Mao-Tsun

    2008-02-15

    This study describes a high-accuracy inclined plane test system for quantitative measurement of the limb motor function of laboratory rats. The system is built around a microcontroller and uses a stepping motor to drive a ball screw, which changes the angle of the inclined plane. Any of the seven inclination speeds can be selected by the user. Two infrared (IR) LED/detector pairs function as interrupt sensors for objective determination of the moment that the rat loses its grip on the textured flooring of the starting area and slips down the plane. Inclination angle at the moment of IR interrupt (i.e. rat slip) is recorded. A liquid crystal display module shows the inclination speed and the inclination angle. The system can function as a stand alone device but a RS232 port allows connection to a personal computer (PC), so data can be sent directly to hard disk for storage and analysis. Experiments can be controlled by a local keypad or by the connected PC. Advantages of the presented system include easy operation, high accuracy, non-dependence on human observation for determination of slip angle, stand-alone capability, low cost and easy modification of the controlling software for different types of experiments. A fully functional prototype of the system is described. The prototype was used experimentally by a hospital group testing traumatic brain injury experiments, and some of their results are presented for system verification. It is found that the system is stable, accurate and easily used by investigators.

  16. Thickness determination of polymeric multilayer surface protection systems for concrete by means of pulse thermography

    Science.gov (United States)

    Altenburg, S. J.; Krankenhagen, R.; Bavendiek, F.

    2017-02-01

    For thickness determination of polymer based surface protection systems for concrete surfaces, so far only destructive measurement techniques are available. Pulse thermography appears to be well suited for non-destructive thickness evaluation in these systems. Here, we present first results of the development of a respective measurement and analysis procedure. Since surface protection systems consist of a number of layers, a model for the calculation of the surface temperature of a multi-layer structure on a semi-infinite (concrete) substrate in pulse thermography setup was developed. It considers semitransparency of the upmost layer and thermal losses at the surface. It also supports the use of an arbitrary temporal shape of the heating pulse to properly describe the measurement conditions for different heat sources. Simulations for one and three layers on the substrate are presented and first results from fitting the model to experimental data for thickness determination and verification of the model are presented.

  17. Development of a System for Absolute Quantum Efficiency Determination of Hybrid Photo Diodes

    CERN Document Server

    Hammarstedt, P

    2001-01-01

    At CERN, the European Laboratory for Particle Physics, a new particle accelerator, the Large Hadron Collider (LHC), is under development. The detectors at LHC require development of highly sophisticated technologies, including Hybrid Photo Diodes (HPD) for high efficiency, high resolution single photon detection with a large area coverage. During the HPD development phase, one of the crucial parameters in the optimization of the photocathode creation process is the quantum efficiency. The aim of this Master Thesis has been to design and implement a system for high precision, high resolution quantum efficiency determination over a large, 200-700 nm photon wavelength range. Commercially available components have been obtained, an optomechanical system has been designed and built, and all the necessary data acquisition, control and analysis software has been implemented. The relative precision of the measurement system has been determined to 2%, with additional possible systematic errors less than 2%. Various qu...

  18. Determination of External Forces in Alpine Skiing Using a Differential Global Navigation Satellite System

    Directory of Open Access Journals (Sweden)

    Erich Müller

    2013-08-01

    Full Text Available In alpine ski racing the relationships between skier kinetics and kinematics and their effect on performance and injury-related aspects are not well understood. There is currently no validated system to determine all external forces simultaneously acting on skiers, particularly under race conditions and throughout entire races. To address the problem, this study proposes and assesses a method for determining skier kinetics with a single lightweight differential global navigation satellite system (dGNSS. The dGNSS kinetic method was compared to a reference system for six skiers and two turns each. The pattern differences obtained between the measurement systems (offset ± SD were −26 ± 152 N for the ground reaction force, 1 ± 96 N for ski friction and −6 ± 6 N for the air drag force. The differences between turn means were small. The error pattern within the dGNSS kinetic method was highly repeatable and precision was therefore good (SD within system: 63 N ground reaction force, 42 N friction force and 7 N air drag force allowing instantaneous relative comparisons and identification of discriminative meaningful changes. The method is therefore highly valid in assessing relative differences between skiers in the same turn, as well as turn means between different turns. The system is suitable to measure large capture volumes under race conditions.

  19. Chemiluminescence Determination of Molybdenum by on-Line Reduction with a Flow Injection System

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The chemiluminescence (CL) reaction between lucigenin (Lu) and molybdenum (Ⅲ) produced by a Jones reductor was investigated using a flow injection system. On the basis of this, a novel method for the determination of trace amount of molybdenum has been established. The emission intensity was linear with molybdenum concentration in the range of 0.1-1000 ng/mL; the detection limit was 0.02 ng/mL molybdenum; the relative standard deviation was less than 2% for the determination of 0.1 ng/mL molybdenum (n=11). The method has been applied successfully to the analysis of trace molybdenum in water and steel samples.

  20. From supernova to Solar System: Few years only; first Solar System components apatite and spinel determined

    Science.gov (United States)

    Jungck, Matthias H. A.; Niederer, Franz R.

    2017-03-01

    We show data for the very first years of our Solar System development after an interaction between undisturbed, cold interstellar dust and supernova type II explosion gases. All manual work was done in 1976-1982 as part of 3 theses works but fundamentally new data interpretation was reached within the last three years. From the CI1 meteorite Orgueil, we are able to separate 1.4 per mill of material containing supernova related noble gases He, Ne and Ar as well as P. We separate minerals using essentially density gradient centrifugation followed by stepwise heating noble gas analysis. Our procedure loses nearly no material and is in sharp contrast to the otherwise used dissolution of >99% of material to obtain single presolar grains (Anders and Zinner, 1993). Our method safeguards minerals considerably more fragile than SiC or TiC presolar grains, such as apatite, Mg-Al-spinel, graphite clusters and even apatite coated graphite clusters. We find graphite, apatite and Mg-Al-spinel containing highly anomalous noble gases. For the first time, apatite, containing anomalous Ar with an isotope ratio for 38Ar/36Ar of 0.35, twice the normal ratio, is reported. Such a ratio is produced by a 20 solar mass type II supernova in the C-O-Ne-burning shell. Unmatched pure Ne-E from 22Na measured in the same samples sets the timeframe for this interaction to a maximum of only a few years.

  1. Signal Processing Scheme for Increasing System Resolution in Determination of the Scattering Position in an OCT System

    Institute of Scientific and Technical Information of China (English)

    SONG Guiju; WANG Xiangzhao; FANG Zujie

    2001-01-01

    In an OCT sensing system, the optical coherence length of the light source determines the spatial resolution, which is within the range of tens of micrometers. In this paper, by removing high-frequency noise with average operation and fitting the measured discrete sampled data with a continuous function, the theoretical resolution can be improved. The experimental results obtained show the short-term repeatability to be better than 0.4 μm after signal processing.

  2. THE DETERMINANTS OF BANKING SYSTEM VULNERABILITY IN THE REPUBLIC OF MOLDOVA

    Directory of Open Access Journals (Sweden)

    Dorina CLICHICI

    2013-12-01

    Full Text Available A banking system is more vulnerable when there are felt more negative effects on this as a consequence of the global financial crisis events. In the context of the objective of enhancing financial stability and, in particular, limiting the likelihood of failure of the banking system it is useful to verify how the main characteristics which play a role for banking system vulnerability behaved in the case of the Republic of Moldova: system’s liquidity, capitalization, competition, diversification, presence of foreign banks, and wholesale funding. In order to determine how hard was hit the banking system of Moldova by the recent financial crisis in the article are analyzed quantitative and qualitative the above mentioned characteristics and identified the crisis effects on them.

  3. Development of interim test methods and procedures for determining the performance of small photovoltaic systems

    Energy Technology Data Exchange (ETDEWEB)

    McNutt, P.; Kroposki, B.; Hansen, R.; Algra, K.; DeBlasio, R. [National Renewable Energy Lab., Golden, CO (United States)

    1998-09-01

    The National Renewable Energy Laboratory (NREL) is developing tests and procedures that will determine if the configuration of a small photovoltaic (PV) system is suitable for its intended use, and if the system will perform as specified. An overview of these procedures is presented in this paper. Development of standard test procedures will allow designers, manufacturers, system integrators, users, and independent laboratories to assess the performance of PV systems under outdoor prevailing conditions. An NREL Technical Report detailing the procedures is under way, and the IEEE Standards Coordinating Committee 21 (SCC21) has established a project on this subject. The work will be submitted to the IEEE SCC21 and International Electrotechnical Commission Technical Committee 82 (IEC TC82) for consideration as a consensus standard. Certification bodies such as PowerMark and PV Global Approval Program (PVGAP) may adopt the IEC and IEEE documents when testing systems. Developing standardized test methods and procedures at NREL to evaluate the outdoor performance of PV systems will encourage product quality and promote PV standards development. Standardized tests will assure people that PV systems will perform as specified for their intended applications. As confidence in PV systems increases, the successful commercialization of PV will grow internationally.

  4. Statistical determinations of the gating windows in the respiratory gated radiotherapy using the visible guiding system

    CERN Document Server

    Oh, Se An; Lee, Hyun Jeong; Kim, Sung Kyu

    2015-01-01

    Purpose: Respiratory gated radiation therapy (RGRT) is used to minimize the radiation dose to normal tissue in lung cancer patients. Determinations of the gating window in the respiratory phase of patients are important in RGRT but it is not easy. The objective of this study was to determine the optimal gating window with a visible guiding system in RGRT. Materials and Methods: Between April and October in 2014 the breathing signals of 23 lung cancer patients were recorded with a Real-time Position Management (RPM) respiratory gating system (Varian, USA). We performed statistical analysis with breathing signals to find the optimal gating window for the guided breathing for RGRT. Results: 19 of the 23 patients showed statistically significant differences (p < 0.05) when the breathing signals obtained before and after breathing training were compared, The standard deviation of the respiration signals after breathing training was the lowest in the phase of 30 % - 70 % (p < 0.05). Conclusions: RGRT with RPM...

  5. A New Method to Determine the Temperature of CMEs Using a Coronagraph Filter System

    CERN Document Server

    Cho, Kyuhyoun; Lim, Eun-kyung; Cho, Kyung-suk; Bong, Su-Chan; Yang, Heesu

    2016-01-01

    The coronagraph is an instrument enables the investigation of faint features in the vicinity of the Sun, particularly coronal mass ejections (CMEs). So far coronagraphic observations have been mainly used to determine the geometric and kinematic parameters of CMEs. Here, we introduce a new method for the determination of CME temperature using a two filter (4025 A and 3934 A) coronagraph system. The thermal motion of free electrons in CMEs broadens the absorption lines in the optical spectra that are produced by the Thomson scattering of visible light originating in the photosphere, which affects the intensity ratio at two different wavelengths. Thus the CME temperature can be inferred from the intensity ratio measured by the two filter coronagraph system. We demonstrate the method by invoking the graduated cylindrical shell (GCS) model for the 3 dimensional CME density distribution and discuss its significance.

  6. Face Synthesis (FASY) System for Determining the Characteristics of a Face Image

    CERN Document Server

    Halder, Santanu; Nasipuri, Mita; Basu, Dipak Kumar; Kundu, Mahantapas

    2010-01-01

    This paper aims at determining the characteristics of a face image by extracting its components. The FASY (FAce SYnthesis) System is a Face Database Retrieval and new Face generation System that is under development. One of its main features is the generation of the requested face when it is not found in the existing database, which allows a continuous growing of the database also. To generate the new face image, we need to store the face components in the database. So we have designed a new technique to extract the face components by a sophisticated method. After extraction of the facial feature points we have analyzed the components to determine their characteristics. After extraction and analysis we have stored the components along with their characteristics into the face database for later use during the face construction.

  7. Determination of production run time and warranty length under system maintenance and trade credits

    Science.gov (United States)

    Tsao, Yu-Chung

    2012-12-01

    Manufacturers offer a warranty period within which they will fix failed products at no cost to customers. Manufacturers also perform system maintenance when a system is in an out-of-control state. Suppliers provide a credit period to settle the payment to manufacturers. This study considers manufacturer's production and warranty decisions for an imperfect production system under system maintenance and trade credit. Specifically, this study uses the economic production quantity to model the decisions under system maintenance and trade credit. These decisions involve how long the production run time and warranty length should be to maximise total profit. This study provides lemmas for the conditions of optimality and develops a theorem and an algorithm for solving the problems described. Numerical examples illustrate the solution procedures and provide a variety of managerial implications. Results show that simultaneously determining production and warranty decisions is superior to only determining production. This study also discusses the effects of the related parameters on manufacturer's decisions and profits. The results of this study are a useful reference for managerial decision-making and administration.

  8. Cataclysmic Variables below the Period Gap: Mass Determinations of 14 Eclipsing Systems

    CERN Document Server

    Savoury, C D J; Dhillon, V S; Marsh, T R; Gaensicke, B T; Copperwheat, C M; Kerry, P; Hickman, R D G; Parsons, S G

    2011-01-01

    We present high-speed, three-colour photometry of the eclipsing cataclysmic variables CTCV 1300, CTCV 2354 and SDSS 1152. All three systems are below the observed "period gap" for cataclysmic variables. For each system we determine the system parameters by fitting a parameterised model to the observed eclipse light curve by chi-squared minimisation. We also present an updated analysis of all other eclipsing systems previously analysed by our group. New donor masses are generally between 1 and 2 sigma of those originally published, with the exception of SDSS 1502 and DV UMa. We note that the donor mass of SDSS 1501 has been revised upwards by 0.024Msun. This system was previously identified as having evolved passed the minimum orbital period for cataclysmic variables, but the new mass determination suggests otherwise. Our new analysis confirms that SDSS 1035 and SDSS 1433 have evolved past the period minimum for cataclysmic variables, corroborating our earlier studies. We find that the radii of donor stars are...

  9. [Development of an automatic pneumatic tourniquet system that determines pressures in synchrony with systolic blood pressure].

    Science.gov (United States)

    Liu, Hongyun; Li, Kaiyuan; Zhang, Zhengbo; Guo, Junyan; Wang, Weidong

    2012-11-01

    The correlation coefficients between arterial occlusion pressure and systolic blood pressure, diastolic blood pressure, limb circumference, body mass etc were obtained through healthy volunteer experiments, in which tourniquet were applied on upper/lower extremities. The prediction equations were derived from the data of experiments by multiple regression analysis. Based on the microprocessor C8051F340, a new pneumatic tourniquet system that can determine tourniquet pressure in synchrony with systolic blood pressure was developed and verified the function and stability of designed system. Results showed that the pneumatic tourniquet which automatically adjusts occlusion pressure in accordance with systolic blood pressure could stop the flow of blood to get a bloodless field.

  10. Post-Katrina juvenile competency determinations: a tale of two systems.

    Science.gov (United States)

    Wills, Cheryl D

    2008-01-01

    Natural disasters such as Hurricane Katrina have resulted in the displacement of families to locations throughout the nation. Juvenile courts have been affected by this mass migration of youths. Post-disaster recovery has been slow. Consequently, a cohort of youths has aged out of the juvenile justice system before their juvenile competency hearings could be held. Some of these young adults now face charges as adults in criminal courts. The author explores what happens when youths awaiting juvenile competency determinations age out of the system and face charges as adults. The evolution of the problem, the current situation, case examples, and possible solutions are reviewed.

  11. ORGANISATIONAL DETERMINANTS INFLUENCING INFORMATION SYSTEMS REIMPLEMENTATION: SOME IMPLICATIONS TO THE DEVELOPING COUNTRIES

    Directory of Open Access Journals (Sweden)

    Sayyen Teoh

    2010-01-01

    Full Text Available This article presents an in-depth study of global Web-based Marketing Decision Support System reimplementation, in a British-based Fast Moving Consumer Goods (FMCG manufacturer. The paper shows that the success of a system implementation can still be marginal even if the organisation understands the key organisational determinants of success and has influence over them. The paper concludes with a discussion of how implementation planning, user need analysis and communication problems could be overcomed and also some implications to the companies in the developing nations.

  12. A Simple Method to Determine if a Music Information Retrieval System is a "Horse"

    DEFF Research Database (Denmark)

    Sturm, Bob L.

    2014-01-01

    . Akin to the controlled experiments designed to test the intellect of the famous horse ``Clever Hans'', we perform two experiments to show how three state-of-the-art music genre recognition (MGR) and music emotion recognition (MER) systems are relying on factors confounded with the ``ground truth......We propose and demonstrate a simple method to determine if a music information retrieval (MIR) system is using factors irrelevant to the task for which it is designed. This is of critical importance to certain use cases, but cannot be accomplished using standard approaches to evaluation in MIR...

  13. Determination of Solid State Solubility of the Components in the Ag-Ge Film System

    Directory of Open Access Journals (Sweden)

    A.A. Minenkov

    2014-11-01

    Full Text Available The efficiency of determination of solid state solubility of the components in the system with an eutectic type of interaction (Ag-Ge by means of measuring the sample electrical resistance during thermal cycling has been shown. Film systems were formed in a vacuum by sequential condensation of components. The solubility curve of germanium in silver, obtained from the study of the samples with silver film thickness of 100 nm, is in good agreement with available literature data. The activation energy of grain-boundary diffusion has been estimated as 0,8 eV.

  14. Determination of Some Heavy-metal-ions Using a Sulfur Ion Modified BZ Oscillating System

    Institute of Scientific and Technical Information of China (English)

    Hua CHEN; Wu YANG; Hong Xia DAI; Xiao Xia WEI; Jie QU; Jin Zhang GAO

    2006-01-01

    A highly sensitive method is developed for the determination of trace amounts of some heavy metal ions in aqueous solution based on the classical Belousov-Zhabotinskii (BZ) oscillating chemical system. Introducing of S2- ion makes the new oscillating system Ce(SO4)2 - KBrO3-CH2(COOH)2 - Na2S - H2SO4 have to a high sensitivity for some heavy metal ions such as Ag+,pb2+, Hg2+, Cd2+, Cu2+and Bi3+ with detection limits down to 10-12 mol. L-1.

  15. Techniques for determining propulsion system forces for accurate high speed vehicle drag measurements in flight

    Science.gov (United States)

    Arnaiz, H. H.

    1975-01-01

    As part of a NASA program to evaluate current methods of predicting the performance of large, supersonic airplanes, the drag of the XB-70 airplane was measured accurately in flight at Mach numbers from 0.75 to 2.5. This paper describes the techniques used to determine engine net thrust and the drag forces charged to the propulsion system that were required for the in-flight drag measurements. The accuracy of the measurements and the application of the measurement techniques to aircraft with different propulsion systems are discussed. Examples of results obtained for the XB-70 airplane are presented.

  16. Phosphite determination in fertilizers after online sequential sample preparation in a flow injection system.

    Science.gov (United States)

    Dametto, Patrícia Roberta; Franzini, Vanessa Pezza; Gomes Neto, José Anchieta

    2007-07-25

    A flow injection spectrophotometric system is proposed for phosphite determination in fertilizers by the molybdenum blue method after the processing of each sample two times on-line without and with an oxidizing step. The flow system was designed to add sulfuric acid or permanganate solutions alternately into the system by simply displacing the injector-commutator from one resting position to another, allowing the determination of phosphate and total phosphate, respectively. The concentration of phosphite is obtained then by difference between the two measurents. The influence of flow rates, sample volume, and dimension of flow line connecting the injector-commutator to the main analytical channel was evaluated. The proposed method was applied to phosphite determination in commercial liquid fertilizers. Results obtained with the proposed FIA system were not statistically different from those obtained by titrimetry at the 95% confidence level. In addition, recoveries within 94 and 100% of spiked fertilizers were found. The relative standard deviation (n = 12) related to the phosphite-converted-phosphate peak alone was determinations per hour, and the reagent consumption was about 6.3 mg of KMnO4, 200 mg of (NH4)6Mo7O24.4H2O, and 40 mg of ascorbic acid per measurement.

  17. Directed Design of Experiments (DOE) for Determining Probability of Detection (POD) Capability of NDE Systems (DOEPOD)

    Science.gov (United States)

    Generazio, Ed

    2007-01-01

    This viewgraph presentation reviews some of the issues that people who specialize in Non destructive evaluation (NDE) have with determining the statistics of the probability of detection. There is discussion of the use of the binominal distribution, and the probability of hit. The presentation then reviews the concepts of Directed Design of Experiments for Validating Probability of Detection of Inspection Systems (DOEPOD). Several cases are reviewed, and discussed. The concept of false calls is also reviewed.

  18. Fourier Method for an Over-Determined Elliptic System with Several Complex Variables

    Institute of Scientific and Technical Information of China (English)

    Dao Qing DAI

    2006-01-01

    Two boundary value problems are investigated for an over-determined elliptic system with several complex variables in polydisc. Necessary and sufficient conditions for the existence of finitely many linearly independent solutions and finitely many solvability conditions are derived. Moreover,the boundary value problem for any number of complex variables is treated in a unified way and the essential difference between the case of one complex variable and that of several complex variables is revealed.

  19. Determination of phase equilibria in the Ni-Ta-Zr system at 1223 K

    Institute of Scientific and Technical Information of China (English)

    PAN Ximiao; JIN Zhanpeng

    2003-01-01

    The phase equilibrium relations of the ternary Ni-Ta-Zr system at 1223 K were investigated by means of diffusion triple and electron probe microanalysis (EPMA) techniques. Two ternary compounds were found and a series of tie lines and fie triangles have been determined. The maximum solubility of Ta in NiZr2 is about 13.5% (atom fraction). The corresponding tentative isothermal section at this temperature was constructed based on current experimental information.

  20. Bias determination for space accelerometers using the ZARM Catapult system - experimental setup and data analysis

    Science.gov (United States)

    Selig, Hanns; Santos Rodrigues, Manuel; Touboul, Pierre; Liorzou, Françoise

    2012-07-01

    Accelerometers for space applications - like the electrostatic differential accelrometer for the MICROSCOPE mission for testing the equivalence principle in space - have to be tested and qualified in μg-conditions in order to demonstrate the system operation and to determine the characteristic sensor parameters. One important characteristic property is the sensor bias. In principle one can determine the sensor bias directly by using the ZARM catapult system as test platform. Even in the evacuated drop tube the residual air pressure results in an air friction that depends on the capsule velocity. At the apex (highest point of the capsule trajectory) the acceleration (relative to the gravitational acceleration g) becomes zero due to the zero velocity at the apex. The direct measurement of the vertical linear acceleration sensor bias is affected by some additional effects that have to be understood in order to be able to determine the sensor bias. Two catapult campaigns have been carried out to demonstrate the principles of the bias determination using a SuperStar accelerometer (Onera). The presentation gives an overview on the experimental setup and on the corresponding data analysis.

  1. The ST5000: An Attitude Determination System with Low-Bandwidth Digital Imaging

    Science.gov (United States)

    Percival, J. W.; Nordsieck, K. H.

    The Space Astronomy Laboratory is building an attitude determination and digital imaging system with embedded compression. The attitude determination system uses a 30-square-degree field of view and an embedded star catalog to determine the Right Ascension and Declination of its line of sight to better than 5 arcseconds. The digital imaging subsystem uses a scheme of ``progressive image transmission'' in which the image is sent out over a very-low-bandwidth channel, such as a spacecraft telemetry downlink, in such a way that it can be reconstructed ``on the fly'' and updated as more data arrive. Large (768×474) useful images can be obtained over a 4-kbit downlink in as little as 10 seconds. In addition to its use in sounding rockets and spacecraft, we are planning to use it for two ground-based applications at the Southern Africa Large Telescope (SALT). We will explore its use in generating real-time measurements of the telescope pointing, independent of the telescope control system, and we will use the low bandwidth imaging capability for public outreach.

  2. METHODOLOGY OF DETERMINATION OF QUALITY INDEX OF MAINTENANCE SERVICE SYSTEM OF POWER EQUIPMENT OF TRACTION SUBSTATIONS

    Directory of Open Access Journals (Sweden)

    O.O. Matusevych

    2016-03-01

    Full Text Available Purpose. The purpose of this paper is development of methodology for definition of a quality system of maintenance and repair (M and P power equipment of traction substations (TS of electrified railways operating under conditions of uncertainty based on expert information. Methodology. The basic tenets of the theory of fuzzy sets and marks, linguistic and interval estimates of experts were applied to solve this problem. Results. Analysis of the existing diversity of approaches to development of modern methods of improvement of M and P allows us to conclude that the improvement in the quality of the system is achieved by solving individual problems increase the operational reliability of power equipment of traction substations in the following main interrelated areas. There are technical, economic and organizational. The basis of the quality evaluation system is initial data and expertise developed version of the document formalized quality evaluation of electrical equipment of traction substations by experts. The choice of determining the level of Quality service system based on the marks, linguistic and interval estimates of experts, which are reflected in quantitative and / or qualitative form was done. The possible options for expert data presentation and their corresponding quantitative methods of calculating the integral index of quality improvement system maintenance and P of traction substations were described. The methodology and the method of assessing the quality of system maintenance and P of TS allows quickly respond to changing operating conditions of power equipment of traction substations, and to determine the most effective strategies for maintenance of electrical and P TS under conditions of uncertainty functioning distance electricity. Originality. The method of a systematic approach to improve the quality of the system maintenance and P of power equipment of traction substation under conditions of uncertainty based on expert

  3. Root–shoot allometry of tropical forest trees determined in a large-scale aeroponic system

    Science.gov (United States)

    Eshel, Amram; Grünzweig, José M.

    2013-01-01

    Background and Aims This study is a first step in a multi-stage project aimed at determining allometric relationships among the tropical tree organs, and carbon fluxes between the various tree parts and their environment. Information on canopy–root interrelationships is needed to improve understanding of above- and below-ground processes and for modelling of the regional and global carbon cycle. Allometric relationships between the sizes of different plant parts will be determined. Methods Two tropical forest species were used in this study: Ceiba pentandra (kapok), a fast-growing tree native to South and Central America and to Western Africa, and Khaya anthotheca (African mahogany), a slower-growing tree native to Central and Eastern Africa. Growth and allometric parameters of 12-month-old saplings grown in a large-scale aeroponic system and in 50-L soil containers were compared. The main advantage of growing plants in aeroponics is that their root systems are fully accessible throughout the plant life, and can be fully recovered for harvesting. Key Results The expected differences in shoot and root size between the fast-growing C. pentandra and the slower-growing K. anthotheca were evident in both growth systems. Roots were recovered from the aeroponically grown saplings only, and their distribution among various diameter classes followed the patterns expected from the literature. Stem, branch and leaf allometric parameters were similar for saplings of each species grown in the two systems. Conclusions The aeroponic tree growth system can be utilized for determining the basic allometric relationships between root and shoot components of these trees, and hence can be used to study carbon allocation and fluxes of whole above- and below-ground tree parts. PMID:23250916

  4. Towards an accurate and precise determination of the solid-solid transition temperature of enantiotropic systems

    Energy Technology Data Exchange (ETDEWEB)

    Herman, Christelle, E-mail: christelle.herman@ulb.ac.b [Universite Libre de Bruxelles, Transfers, Interfaces and Processes Department, Chemical Engineering Unit, 50 Avenue Franklin D-Roosevelt, CP 165/67, 1050 Bruxelles (Belgium); Leyssens, Tom [Universite Catholique de Louvain, Institute of Condensed Matter and Nanosciences, 1 Place Louis Pasteur, 1348 Louvain-La-Neuve (Belgium); Vermylen, Valerie [UCB Pharma, 60 Allee de la Recherche, 1070 Braine l' Alleud (Belgium); Halloin, Veronique; Haut, Benoit [Universite Libre de Bruxelles, Transfers, Interfaces and Processes Department, Chemical Engineering Unit, 50 Avenue Franklin D-Roosevelt, CP 165/67, 1050 Bruxelles (Belgium)

    2011-05-15

    Research highlights: We test two methods to obtain the solid-solid transition temperature of Etiracetam system, showing two enantiotropically related polymorphs. The first method, based on a thermodynamic development, is sensitive to the correctness of the data required. The second method is an experimental study of the stability thermal range of each morph. We identify the nature of crystals in suspension at equilibrium through Raman analysis. The solid-solid transition temperature is found equal to 303.65 K {+-} 0.5 K. - Abstract: This paper presents two distinct methods for the determination of the solid-solid transition temperature (T{sub tr}) separating the temperature ranges of stability of two crystallographic forms, hereafter called morphs, of a same substance. The first method, based on thermodynamic calculations, consists in determining T{sub tr} as the temperature at which the Gibbs free energies of the two morphs are equal to each other. For this purpose, some thermodynamic characteristics of both morphs are required, such as the specific heat capacities, the melting temperatures and the melting enthalpies. These are obtained using the Differential Scanning Calorimetry (DSC). In the second method, T{sub tr} is determined directly by an experimental study of the temperature ranges of stability of each morph. The three main originalities of the method developed are (i) to prepare samples composed by an isomassic mixture of crystals of both morphs, (ii) to set them in a thermostated and agitated suspension, and (iii) to use an in situ Raman spectroscopic probe for the determination of the crystallographic form of the crystals in suspension at equilibrium. Both methods are applied to determine the solid-solid transition temperature of the enantiotropic system of Etiracetam, and both of its two crystallographic forms so far identified, named morph I and morph II. The first method is shown to be very sensitive to the experimental data obtained by DSC while

  5. Characterization of integrons and tetracycline resistance determinants in Aeromonas spp. isolated from South African aquaculture systems.

    Science.gov (United States)

    Jacobs, Liezl; Chenia, Hafizah Y

    2007-03-20

    An increasing incidence of multidrug resistance amongst Aeromonas spp. isolates, which are both fish pathogens and emerging opportunistic human pathogens, has been observed worldwide. This can be attributed to the horizontal transfer of mobile genetic elements, viz.: plasmids and class 1 integrons. The antimicrobial susceptibilities of 37 Aeromonas spp. isolates, from tilapia, trout and koi aquaculture systems, were determined by disc-diffusion testing. The plasmid content of each isolate was examined using the alkaline lysis protocol. Tet determinant type was determined by amplification using two degenerate primer sets and subsequent HaeIII restriction. The presence of integrons was determined by PCR amplification of three integrase genes, as well as gene cassettes, and the qacEDelta1-sulI region. Thirty-seven Aeromonas spp. isolates were differentiated into six species by aroA PCR-RFLP, i.e., A. veronii biovar sobria, A. hydrophila, A. encheleia, A. ichtiosoma, A. salmonicida, and A. media. High levels of resistance to tetracycline (78.3%), amoxicillin (89.2%), and augmentin (86.5%) were observed. Decreased susceptibility to erythromycin was observed for 67.6% of isolates. Although 45.9% of isolates displayed nalidixic acid resistance, majority of isolates were susceptible to the fluoroquinolones. The MAR index ranged from 0.12 to 0.59, with majority of isolates indicating high-risk contamination originating from humans or animals where antibiotics are often used. Plasmids were detected in 21 isolates, with 14 of the isolates displaying multiple plasmid profiles. Single and multiple class A family Tet determinants were observed in 27% and 48.7% of isolates, respectively, with Tet A being the most prevalent Tet determinant type. Class 1 integron and related structures were amplified and carried different combinations of the antibiotic resistance gene cassettes ant(3'')Ia, aac(6')Ia, dhfr1, oxa2a and/or pse1. Class 2 integrons were also amplified, but the

  6. A numerical method to determine the steady state distribution of passive contaminant in generic ventilation systems.

    Science.gov (United States)

    Li, Xianting; Shao, Xiaoliang; Ma, Xiaojun; Zhang, Yuanhui; Cai, Hao

    2011-08-15

    Ventilation system with air recirculation is designed to conserve energy, yet at the same time may result in transporting hazardous substance among different rooms in the same building, which is a concern in indoor air quality control. There is a lack of effective methods to predict indoor contaminant distribution primarily because of uncertainty of the contaminant concentration in supply air which in turn due to the mixing ratio of fresh and recirculation air. In this paper, a versatile numerical method to determine the pollutant distribution of ventilation system with recirculation at steady state is proposed based on typical ventilation systems with accessibility of supply air (ASA) and accessibility of contaminant source (ACS). The relationship is established between contaminant concentrations of supply air and return air in a ventilated room or zone. The concentrations of supply air and contaminant distribution in each room can be determined using such parameters as ASA and ACS. The proposed method is validated by both experimental data and numerical simulation result. The computing speed of the proposed method is compared with the iteration method. The comparisons between the proposed method and the lumped parameter model are also conducted. The advantages of the proposed method in terms of accuracy, speed and versatility make it advantageous to be applied in air quality control of complex ventilation systems with recirculation.

  7. A spectrophotometric flow injection system for streptomycin determination in veterinary samples

    Science.gov (United States)

    Frugeri, Pedro Marcos; Lago, Ayla Campos do; Wisniewski, Célio; Luccas, Pedro Orival

    2014-01-01

    In this work a spectrophotometric flow injection analysis system for streptomycin determination in veterinary samples, is being proposed. The method is based on streptomycin alkaline hydrolysis that forms guanidine, followed by the reaction with Fe(II). The colored product has absorption peak at 520 nm. To evaluate and optimize the system parameters, chemometrics tools, such as factorial design, Pareto chart and Doelhert design, were used. The veterinary samples are diluted in water and introduced in the FIA system, therefore no sample preparation is required. The optimized system presented: linear range of 60 up to 1000 mg L-1, limit of detection of 18 mg L-1 and sampling rate of 36 readings per hour. The precision was checked and the CV for veterinary sample readings were always less than 6.5%. The accuracy was studied by comparison with chromatographic method, thus, five samples of pharmaceutical veterinary were determined by HPLC and by the proposed method, and the results are in agreement (t-test, p = 0.05).

  8. What Determines Social Capital in a Social-Ecological System? Insights from a Network Perspective

    Science.gov (United States)

    Barnes-Mauthe, Michele; Gray, Steven Allen; Arita, Shawn; Lynham, John; Leung, PingSun

    2015-02-01

    Social capital is an important resource that can be mobilized for purposive action or competitive gain. The distribution of social capital in social-ecological systems can determine who is more productive at extracting ecological resources and who emerges as influential in guiding their management, thereby empowering some while disempowering others. Despite its importance, the factors that contribute to variation in social capital among individuals have not been widely studied. We adopt a network perspective to examine what determines social capital among individuals in social-ecological systems. We begin by identifying network measures of social capital relevant for individuals in this context, and review existing evidence concerning their determinants. Using a complete social network dataset from Hawaii's longline fishery, we employ social network analysis and other statistical methods to empirically estimate these measures and determine the extent to which individual stakeholder attributes explain variation within them. We find that ethnicity is the strongest predictor of social capital. Measures of human capital (i.e., education, experience), years living in the community, and information-sharing attitudes are also important. Surprisingly, we find that when controlling for other factors, industry leaders and formal fishery representatives are generally not well connected. Our results offer new quantitative insights on the relationship between stakeholder diversity, social networks, and social capital in a coupled social-ecological system, which can aid in identifying barriers and opportunities for action to overcome resource management problems. Our results also have implications for achieving resource governance that is not only ecologically and economically sustainable, but also equitable.

  9. Enzymatic Microreactors for the Determination of Ethanol by an Automatic Sequential Injection Analysis System

    Science.gov (United States)

    Alhadeff, Eliana M.; Salgado, Andrea M.; Cos, Oriol; Pereira, Nei; Valdman, Belkis; Valero, Francisco

    A sequential injection analysis system with two enzymatic microreactors for the determination of ethanol has been designed. Alcohol oxidase and horseradish peroxidase were separately immobilized on glass aminopropyl beads, and packed in 0.91-mL volume microreactors, working in line with the sequential injection analysis system. A stop flow of 120 s was selected for a linear ethanol range of 0.005-0.04 g/L±0.6% relative standard deviation with a throughput of seven analyses per hour. The system was applied to measure ethanol concentrations in samples of distilled and nondistilled alcoholic beverages, and of alcoholic fermentation with good performance and no significant difference compared with other analytical procedures (gas chromatography and high-performance liquid chromatography).

  10. Computer-operated analytical platform for the determination of nutrients in hydroponic systems.

    Science.gov (United States)

    Rius-Ruiz, F Xavier; Andrade, Francisco J; Riu, Jordi; Rius, F Xavier

    2014-03-15

    Hydroponics is a water, energy, space, and cost efficient system for growing plants in constrained spaces or land exhausted areas. Precise control of hydroponic nutrients is essential for growing healthy plants and producing high yields. In this article we report for the first time on a new computer-operated analytical platform which can be readily used for the determination of essential nutrients in hydroponic growing systems. The liquid-handling system uses inexpensive components (i.e., peristaltic pump and solenoid valves), which are discretely computer-operated to automatically condition, calibrate and clean a multi-probe of solid-contact ion-selective electrodes (ISEs). These ISEs, which are based on carbon nanotubes, offer high portability, robustness and easy maintenance and storage. With this new computer-operated analytical platform we performed automatic measurements of K(+), Ca(2+), NO3(-) and Cl(-) during tomato plants growth in order to assure optimal nutritional uptake and tomato production.

  11. Definisanje ekvivalentnog torzionooscilatornog sistema / Determination of the equivalent torsional vibration system

    Directory of Open Access Journals (Sweden)

    Dragan R. Trifković

    2010-07-01

    Full Text Available U radu je prikazan postupak zamene elemenata kompleksnog torzionooscilatornog sistema brodske dizelmotorne propulzije uprošćenim ekvivalentnim elementima istih dinamičkih karakteristika. Izloženi postupak sadrži metode za određivanje ekvivalentnih dužina, krutosti i momenata inercije na osnovu jednakosti kinetičkih i potencijalnih energija realnih i ekvivalentnih elemenata sistema. Osim toga, analizirani su pobudni momenti koji izazivaju prinudne torzione oscilacije razmatranog sistema. / The procedure of replacing the elements of a complex torsional vibration system of ship diesel engine propulsion with simplified equivalent ones with the same dynamic characteristics is shown in this work. The given procedure comprises the methods for the determination of equivalent lengths, stifnesses and moments of inertia based on the equality between kinetic and potential energy of real and equivalent elements of the system. Additionally, the exciting moments which excite forced torsional vibrations of the considered system are analysed.

  12. Phase diagram determination and thermodynamic modeling of the Cu-Mg-Si system

    Directory of Open Access Journals (Sweden)

    Zhao J.

    2016-01-01

    Full Text Available 13 ternary Cu-Mg-Si alloys were prepared by means of the powder metallurgy method. Phase equilibria at 500 and 700 oC of the Cu-Mg-Si system were determined using X-ray diffraction analysis (XRD. The existence of 3 ternary compounds in this system was verified: CuMgSi_Sigma (Cu16Mg6Si7, Tau (Cu3Mg2Si, and Laves ((Cu0.8Si0.22(Mg0.88Cu0.12. A thermodynamic modeling for the Cu-Mg-Si system was then conducted on the basis of the experimental data obtained in this work and those critically reviewed from the literature. The complex phase relationship between Laves phase and other phases has been successfully modeled in this work. Comparisons between the calculated and the measured phase diagrams show that most of the experimental data can be reproduced by the presently obtained thermodynamic parameters.

  13. Determination of Duty Cycle for Energy Storage Systems in a PV Smoothing Application

    Energy Technology Data Exchange (ETDEWEB)

    Schoenwald, David A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Ellison, James [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2016-04-01

    This report supplements the document, "Protocol for Uniformly Measuring and Expressing the Performance of Energy Storage Systems," issued in a revised version in April 2016 (see [4]), which will include the photovoltaic (PV) smoothing application for an energy storage system (ESS). This report provides the background and documentation associated with the determination of a duty cycle for an ESS operated in a PV smoothing application for the purpose of measuring and expressing ESS performance in accordance with the ESS performance protocol. ACKNOWLEDGEMENTS The authors gratefully acknowledge the support of Dr. Imre Gyuk, program manager for the DOE Energy Storage Systems Program. The authors would also like to express their appreciation to all the stakeholders who participated as members of the PV Smoothing Subgroup. Without their thoughtful input and recommendations, the definitions, metrics, and duty cycle provided in this report would not have been possible. A complete listing of members of the PV Smoothing Subgroup appears in the first chapter of this report. Special recognition should go to the staffs at Pacific Northwest National Laboratory (PNNL) and Sandia National Laboratories (SNL) in collaborating on this effort. In particular, Mr. David Conover and Dr. Vish Viswanathan of PNNL and Dr. Summer Ferreira of SNL were especially helpful in their suggestions for the determination of a duty cycle for the PV Smoothing application.

  14. Flow-injection determination of isoniazid using sodium dichloroisocyanurate- and trichloroisocyanuric acid-luminol chemiluminescence systems.

    Science.gov (United States)

    Safavi, A; Karimi, M A; Hormozi Nezhad, M R

    2004-06-01

    A chemiluminescent (CL) method for the determination of isoniazid is described. The method is based on the CL generated during the oxidation of luminol by sodium dichloroisocyanurate (SDCC) and trichloroisocyanuric acid (TCCA) in alkaline medium. It was found that isoniazid greatly enhances this CL intensity when present in the luminol solution. Based on this observation, a new flow-injection CL method for the determination of isoniazid has been proposed in this paper. The detection limits were 2 and 3 ng ml(-1) isoniazid for the SDCC-luminol and TCCA-luminol CL systems, respectively. The relative CL intensity was linear with the isoniazid concentration in the range of 4-100 and 100-200 ng ml(-1) for the SDCC-luminol CL system, and 6-200 and 200-1000 ng ml(-1) for the TCCA-luminol CL system. The results obtained for the assay of pharmaceutical preparations compared well with those obtained by the official methods and demonstrated good accuracy and precision.

  15. Development of a bioassay system for human growth hormone determination with close correlation to immunoassay.

    Science.gov (United States)

    Maimaiti, M; Tanahashi, Y; Mohri, Z; Fujieda, K

    2012-09-01

    Serum growth hormone (GH) level is measured largely through immunoassays in clinical practice. However, a few cases with bioinactive and immunoreactive GH have also been reported. We describe here a new bioassay system for GH determination using the BaF/GM cell line, which proliferates in a dose-dependent manner on hGH addition; cell proliferation was blocked by anti-hGH antibody. This bioassay had the lowest detection limit (∼0.02 ng/ml) reported thus far and the highest specificity for GH. The bioassay results were compared with those of an immunoradiometric assay across 163 patient samples in various endocrine states. A close correlation (the ratio of bioactivity/immunoreactivity was 1.04 ± 0.33, mean ± SD) was observed between bioactivity and immunoreactivity in these samples. The newly developed system is a specific, sensitive, easy, and fast bioassay system for GH determination; we consider it useful for evaluating GH bioactivity in various endocrine states.

  16. Development of microbial engineered whole-cell systems for environmental benzene determination.

    Science.gov (United States)

    Di Gennaro, P; Bruzzese, N; Anderlini, D; Aiossa, M; Papacchini, M; Campanella, L; Bestetti, G

    2011-03-01

    This paper reports the development of two recombinant bacterial systems that can be used to monitor environmental benzene contamination based on Escherichia coli, which carry genes coding for benzene dioxygenase and benzene dihydrodiol dehydrogenase from Pseudomonas putida MST. E. coli strains express these two enzymes under the control of the Ptac promoter or without any induction. These activities can be detected electrochemically or colorimetrically and used to monitor benzene pollution in environmental air samples collected from an oil refinery assessing benzene by different laboratory experimental procedures. The procedures involving whole-cell bioassays determine the concentration of benzene through benzene dioxygenase activity, which allows for direct correlation of oxygen consumption, and through the benzene dihydrodiol dehydrogenase that causes catechol accumulation and restores NADH necessary for the activity of the first enzyme. Oxygen consumption and catechol production deriving from both enzymatic activities are related to benzene concentration and their measurements determined the sensitivity of the system. The results indicated that the sensitivity was enough to detect the benzene vapor at a lower concentration level of 0.01 mM in about 30 min. The possibility for on-line monitoring of benzene concentration by our new recombinant cells results from the fact that no particular treatment of environmental samples is required. This is a major advantage over other biosensors or assays. Moreover, the development of microbial cells that did not require any addition or effectors for the transcription of the specific enzymes, allowed these systems to be more versatile in automated environmental benzene monitoring.

  17. Height Determination Techniques for the Next National Height System of Finland- A Case Study

    Science.gov (United States)

    Saari, T.; Saaranen, V.; Kaartinen, H.; Poutanen, M.; Kukko, A.; Nyberg, S.

    2014-11-01

    Precise levelling is known for its accuracy and reliability in height determination, but the process itself is slow, laborious and expensive. FGI has started a project to develop methods for height determination that could decrease the creation time of national height systems without losing the required accuracy. In this pilot project, we studied precise levelling and alternative techniques: MLS (Mobile Laser Scanning) and GNSS (Global Navigation Satellite System) levelling, which included static GPS (Global Positioning System) and VRS (Virtual Reference Station) measurements.We compared the techniques in a field test, where the height difference of two known benchmarks were measured. All of the height differences were within 16 mm from each other, where the results from the precise levelling and the GPS levelling differed from 0.5-1.0 mm. Results from the MLS measurements were more than 5.0 mm off from the others and the average of the VRS measurements was 10.0 mm off. The uncertainties are compatible with the results, since the largest RMS values were calculated from the MLS and the VRS measurements.This research highlighted the differences of the techniques, but none of them is yet to be abandoned. The study should be expanded into a larger scale to better evaluate strengths and weaknesses of the techniques.

  18. Hight Determination Techniques for the Next National Height System of Finland- A Case Study

    Science.gov (United States)

    Saari, T.; Saaranen, V.; Kaartinen, H.; Poutanen, M.; Kukko, A.; Nyberg, S.

    2014-11-01

    Precise levelling is known for its accuracy and reliability in height determination, but the process itself is slow, laborious and expensive. FGI has started a project to develop methods for height determination that could decrease the creation time of national height systems without losing the required accuracy. In this pilot project, we studied precise levelling and alternative techniques: MLS (Mobile Laser Scanning) and GNSS (Global Navigation Satellite System) levelling, which included static GPS (Global Positioning System) and VRS (Virtual Reference Station) measurements. We compared the techniques in a field test, where the height difference of two known benchmarks were measured. All of the height differences were within 16 mm from each other, where the results from the precise levelling and the GPS levelling differed from 0.5-1.0 mm. Results from the MLS measurements were more than 5.0 mm off from the others and the average of the VRS measurements was 10.0 mm off. The uncertainties are compatible with the results, since the largest RMS values were calculated from the MLS and the VRS measurements. This research highlighted the differences of the techniques, but none of them is yet to be abandoned. The study should be expanded into a larger scale to better evaluate strengths and weaknesses of the techniques.

  19. Determination of phase equilibria in confined systems by open pore cell Monte Carlo method.

    Science.gov (United States)

    Miyahara, Minoru T; Tanaka, Hideki

    2013-02-28

    We present a modification of the molecular dynamics simulation method with a unit pore cell with imaginary gas phase [M. Miyahara, T. Yoshioka, and M. Okazaki, J. Chem. Phys. 106, 8124 (1997)] designed for determination of phase equilibria in nanopores. This new method is based on a Monte Carlo technique and it combines the pore cell, opened to the imaginary gas phase (open pore cell), with a gas cell to measure the equilibrium chemical potential of the confined system. The most striking feature of our new method is that the confined system is steadily led to a thermodynamically stable state by forming concave menisci in the open pore cell. This feature of the open pore cell makes it possible to obtain the equilibrium chemical potential with only a single simulation run, unlike existing simulation methods, which need a number of additional runs. We apply the method to evaluate the equilibrium chemical potentials of confined nitrogen in carbon slit pores and silica cylindrical pores at 77 K, and show that the results are in good agreement with those obtained by two conventional thermodynamic integration methods. Moreover, we also show that the proposed method can be particularly useful for determining vapor-liquid and vapor-solid coexistence curves and the triple point of the confined system.

  20. Systems biology approaches and pathway tools for investigating cardiovascular disease

    NARCIS (Netherlands)

    Wheelock, C.E.; Wheelock, A.M.; Kawashima, S.; Diez, D.; Kanehisa, M.; Erk, M. van; Kleemann, R.; Haeggström, J.Z.; Goto, S.

    2009-01-01

    Systems biology aims to understand the nonlinear interactions of multiple biomolecular components that characterize a living organism. One important aspect of systems biology approaches is to identify the biological pathways or networks that connect the differing elements of a system, and examine ho

  1. Low-cost attitude determination system using an extended Kalman filter (EKF) algorithm

    Science.gov (United States)

    Esteves, Fernando M.; Nehmetallah, Georges; Abot, Jandro L.

    2016-05-01

    Attitude determination is one of the most important subsystems in spacecraft, satellite, or scientific balloon mission s, since it can be combined with actuators to provide rate stabilization and pointing accuracy for payloads. In this paper, a low-cost attitude determination system with a precision in the order of arc-seconds that uses low-cost commercial sensors is presented including a set of uncorrelated MEMS gyroscopes, two clinometers, and a magnetometer in a hierarchical manner. The faster and less precise sensors are updated by the slower, but more precise ones through an Extended Kalman Filter (EKF)-based data fusion algorithm. A revision of the EKF algorithm fundamentals and its implementation to the current application, are presented along with an analysis of sensors noise. Finally, the results from the data fusion algorithm implementation are discussed in detail.

  2. SIMULTANEOUS DETERMINATION OF CHLORINE DIOXIDE AND HYPOCHLOROUS ACID IN BLEACHING SYSTEM

    Directory of Open Access Journals (Sweden)

    Qiang Wang

    2011-04-01

    Full Text Available This study has demonstrated a rapid spectroscopic method for the determination of chlorine dioxide and hypochlorous acid concentrations in the pulp bleaching processes. It was found that chlorine dioxide and hypochlorous acid have an isosbestic wavelength of 295 nm. The soluble lignin in such a system is the main interference, but can be corrected by determining the absorbances at 295 nm, 380 nm, and 480 nm. Thus, based on the spectroscopic measurements at 295 nm (the isosbestic point wavelength for chlorine dioxide and hypochlorous acid, 380 nm (absorbance wavelength of chlorine dioxide and 480 nm (the acid soluble lignin absorbance wavelength, the chlorine dioxide and hypochlorous acid concentrations in the bleaching process can be quantified. However, hypochlorous acid was not detected in the real bleaching effluent for its low content. The present method is simple, rapid, accurate, and has the potential for on-line monitoring of the chlorine dioxide bleaching process.

  3. The in vitro effect of drugs on biochemical parameters determined by a SMAC system.

    Science.gov (United States)

    Vinet, B; Letellier, G

    1977-02-01

    1. We have studied the in vitro effect of 39 drugs on 17 biochemical parameters determined by a SMAC System. Only two drugs were found to interfere: ascorbic and theophyline. 2. The ascorbic acid lowers the glucose and the bilirubine values; it increases the creatinine and the uric acid concentration. At concentration smaller than 5 mg/dl of this drug, these effects are negligible. 3. We have found a new drug interference: theophylline inhibits the alkaline phosphatase and LDH activities. This effect is not negligible on alkaline phosphatase for therapeutic levels of this drug; the action on LDH can be ignored at normal therapeutic range. 4. For a given drug, we have found different interference with biochemical parameters determined with various commercial lyophlised control sera or a liquid pool of sera. This indicates that the type of sera used in drug interference studies must be described.

  4. Validated spectrofluorometric method for determination of gemfibrozil in self nanoemulsifying drug delivery systems (SNEDDS)

    Science.gov (United States)

    Sierra Villar, Ana M.; Calpena Campmany, Ana C.; Bellowa, Lyda Halbaut; Trenchs, Monserrat Aróztegui; Naveros, Beatriz Clares

    2013-09-01

    A spectrofluorometric method has been developed and validated for the determination of gemfibrozil. The method is based on the excitation and emission capacities of gemfibrozil with excitation and emission wavelengths of 276 and 304 nm respectively. This method allows de determination of the drug in a self-nanoemulsifying drug delivery system (SNEDDS) for improve its intestinal absorption. Results obtained showed linear relationships with good correlation coefficients (r2 > 0.999) and low limits of detection and quantification (LOD of 0.075 μg mL-1 and LOQ of 0.226 μg mL-1) in the range of 0.2-5 μg mL-1, equally this method showed a good robustness and stability. Thus the amounts of gemfibrozil released from SNEDDS contained in gastro resistant hard gelatine capsules were analysed, and release studies could be performed satisfactorily.

  5. Automatic ultrasonic inspection system for wear determination in calandria tubes of Embalse Nuclear Power Plant

    Science.gov (United States)

    Katchadjian, Pablo; Desimone, Carlos; Garcia, Alejandro; Antonaccio, Carlos; Schroeter, Fernando; Molina, Héctor

    2015-03-01

    Embalse Nuclear Power Plant (CNE) (CANDU design) is reaching its end of life and due to elapsed operating time the problem of deformation by accelerated creep occurs in the pressure tubes (PT), leading to a possible contact between calandria tubes (CT), concentric to the PT, and some Liquid Injection Shutdown System (LISS) nozzles that pass underneath them. With determination of CT wear, after the predicted contact occurs, the wear rate of the TC could be determined and thus take less conservative measures over the remaining life of the component. This paper presents the development of an ultrasonic technique for measuring wear in CT, with nominal thickness of 1.34 mm. Because the only access is through the interior of PT, to perform this measurement it is necessary to pass through three different interfaces.

  6. Determining the sub-Lyapunov exponent of delay systems from time series.

    Science.gov (United States)

    Jüngling, Thomas; Soriano, Miguel C; Fischer, Ingo

    2015-06-01

    For delay systems the sign of the sub-Lyapunov exponent (sub-LE) determines key dynamical properties. This includes the properties of strong and weak chaos and of consistency. Here we present a robust algorithm based on reconstruction of the local linearized equations of motion, which allows for calculating the sub-LE from time series. The algorithm is inspired by a method introduced by Pyragas for a nondelayed drive-response scheme [K. Pyragas, Phys. Rev. E 56, 5183 (1997)]. In the presented extension to delay systems, the delayed feedback takes over the role of the drive, whereas the response of the low-dimensional node leads to the sub-Lyapunov exponent. Our method is based on a low-dimensional representation of the delay system. We introduce the basic algorithm for a discrete scalar map, extend the concept to scalar continuous delay systems, and give an outlook to the case of a full vector-state system, from which only a scalar observable is recorded.

  7. Orbit determination and orbit control for the Earth Observing System (EOS) AM spacecraft

    Science.gov (United States)

    Herberg, Joseph R.; Folta, David C.

    1993-01-01

    Future NASA Earth Observing System (EOS) Spacecraft will make measurements of the earth's clouds, oceans, atmosphere, land and radiation balance. These EOS Spacecraft will be part of the NASA Mission to Planet Earth. This paper specifically addresses the EOS AM Spacecraft, referred to as 'AM' because it has a sun-synchronous orbit with a 10:30 AM descending node. This paper describes the EOS AM Spacecraft mission orbit requirements, orbit determination, orbit control, and navigation system impact on earth based pointing. The EOS AM Spacecraft will be the first spacecraft to use the TDRSS Onboard Navigation System (TONS) as the primary means of navigation. TONS flight software will process one-way forward Doppler measurements taken during scheduled TDRSS contacts. An extended Kalman filter will estimate spacecraft position, velocity, drag coefficient correction, and ultrastable master oscillator frequency bias and drift. The TONS baseline algorithms, software, and hardware implementation are described in this paper. TONS integration into the EOS AM Spacecraft Guidance, Navigation, and Control (GN&C) System; TONS assisted onboard time maintenance; and the TONS Ground Support System (TGSS) are also addressed.

  8. Determination of The Mechanical Power in Belt Conveyor's Drive System in Industrial Conditions

    Science.gov (United States)

    Król, Robert; Kaszuba, Damian; Kisielewski, Waldemar

    2016-10-01

    Mechanical power is a value which carries a significant amount of information on the properties of the operating status of the machine analysed. The value of mechanical power reflects the degree of load of the drive system and of the entire machine. It is essential to determine the actual efficiency of the drive system η [%], which is the key parameter of the energy efficiency of the drive system. In the case of a single drive of a belt conveyor the actual efficiency is expressed as the ratio of mechanical output power Pm [W] at the drive pulley shaft to active electrical power drawn by the motor Pe [W]. Furthermore, the knowledge about the mechanical power from all drives of the multiple driven belt conveyor allows for the analysis of load distribution between the drives. In case of belt conveyor, the mechanical power Pm [W] generated by the drive at the drive pulley's shaft is equal to its angular velocity ω [rad / s] multiplied by the torque T [Nm]. The measurement of angular velocity is relatively easy and can be realized with the use of a tachometer or can be determined on the basis of linear velocity of the conveyor belt during belt conveyor's steady state operation. Significantly more difficult to perform in industrial conditions is the measurement of the torque. This is due to the operational conditions of belt conveyors (e.g. dustiness, high humidity, high temperature) and tight assembly of the drive components without the possibility of their disassembly. It makes it difficult or even impossible to measure the torque using a number of the techniques available, causing an individual approach to each object of research. The paper proposes a measurement methodology allowing to determine the mechanical power in belt conveyors drives which are commonly used in underground and surface mining. The paper presents result of the research into mechanical power in belt conveyor's drive carried out in underground mine conditions.

  9. Determination of the critical micelle concentration in simulations of surfactant systems

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Andrew P.; Panagiotopoulos, Athanassios Z., E-mail: azp@princeton.edu [Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544 (United States)

    2016-01-28

    Alternative methods for determining the critical micelle concentration (cmc) are investigated using canonical and grand canonical Monte Carlo simulations of a lattice surfactant model. A common measure of the cmc is the “free” (unassociated) surfactant concentration in the presence of micellar aggregates. Many prior simulations of micellizing systems have observed a decrease in the free surfactant concentration with overall surfactant loading for both ionic and nonionic surfactants, contrary to theoretical expectations from mass-action models of aggregation. In the present study, we investigate a simple lattice nonionic surfactant model in implicit solvent, for which highly reproducible simulations are possible in both the canonical (NVT) and grand canonical (μVT) ensembles. We confirm the previously observed decrease of free surfactant concentration at higher overall loadings and propose an algorithm for the precise calculation of the excluded volume and effective concentration of unassociated surfactant molecules in the accessible volume of the solution. We find that the cmc can be obtained by correcting the free surfactant concentration for volume exclusion effects resulting from the presence of micellar aggregates. We also develop an improved method for determination of the cmc based on the maximum in curvature for the osmotic pressure curve determined from μVT simulations. Excellent agreement in cmc and other micellar properties between NVT and μVT simulations of different system sizes is observed. The methodological developments in this work are broadly applicable to simulations of aggregating systems using any type of surfactant model (atomistic/coarse grained) or solvent description (explicit/implicit)

  10. Determinants of the energy price system in the Federal Republic of Germany

    Energy Technology Data Exchange (ETDEWEB)

    Hennicke, P.

    1983-01-01

    The seven theses presented in this article are to illustrate some basic determinants of the West German energy price system systematically and - at present mainly - empirically. The theses are related to the following sub-aspects: - relation between the consumption structure of primary energy and the heat-price relations, - influence of energy imports on the domestic energy price level, - existence and dimensions of differential revenues, - reproaches of bulling made to the petroleum industry, - extent and development of the differentiation of energy prices, - influence of governmental interventions on the energy price level, - theoretical price fixing principles and actual tariff policy.

  11. Optimal Determination of Respiratory Airflow Patterns Using a Nonlinear Multicompartment Model for a Lung Mechanics System

    Directory of Open Access Journals (Sweden)

    Hancao Li

    2012-01-01

    Full Text Available We develop optimal respiratory airflow patterns using a nonlinear multicompartment model for a lung mechanics system. Specifically, we use classical calculus of variations minimization techniques to derive an optimal airflow pattern for inspiratory and expiratory breathing cycles. The physiological interpretation of the optimality criteria used involves the minimization of work of breathing and lung volume acceleration for the inspiratory phase, and the minimization of the elastic potential energy and rapid airflow rate changes for the expiratory phase. Finally, we numerically integrate the resulting nonlinear two-point boundary value problems to determine the optimal airflow patterns over the inspiratory and expiratory breathing cycles.

  12. Optimal determination of respiratory airflow patterns using a nonlinear multicompartment model for a lung mechanics system.

    Science.gov (United States)

    Li, Hancao; Haddad, Wassim M

    2012-01-01

    We develop optimal respiratory airflow patterns using a nonlinear multicompartment model for a lung mechanics system. Specifically, we use classical calculus of variations minimization techniques to derive an optimal airflow pattern for inspiratory and expiratory breathing cycles. The physiological interpretation of the optimality criteria used involves the minimization of work of breathing and lung volume acceleration for the inspiratory phase, and the minimization of the elastic potential energy and rapid airflow rate changes for the expiratory phase. Finally, we numerically integrate the resulting nonlinear two-point boundary value problems to determine the optimal airflow patterns over the inspiratory and expiratory breathing cycles.

  13. Determining optimal pattern sequences for three-dimensional structured light sensory systems.

    Science.gov (United States)

    Marin, Veronica E; Nejat, Goldie

    2016-04-20

    Structured light (SL) techniques are used for three-dimensional (3D) measurements of objects in a wide variety of applications. SL-based sensory systems obtain the 3D surface profile of an object from the deformation of light patterns projected onto the object of interest. The number of fringes used in the projected light patterns has a direct effect on the 3D reconstruction errors. This paper presents a novel methodology for determining the optimal sequence of multi-fringe patterns that minimizes reconstruction errors caused by random noise. Experiments conducted with a variety of objects as well as a comparison study demonstrate the effectiveness of the proposed methodology.

  14. New methods for determining speciality of linear systems based at fat points in P^n

    CERN Document Server

    Paul, Stepan

    2012-01-01

    In this paper we develop techniques for determining the dimension of linear systems of divisors based at a collection of general fat points in P^n by partitioning the monomial basis for the vector space of global sections of O(d). The methods we develop can be viewed as extensions of those developed by Dumnicki. We apply these techniques to produce new lower bounds on multi-point Seshadri constants of P^2 and to provide a new proof of a known result confirming the perfect-power cases of Iarrobino's analogue to Nagata's Conjecture in higher dimension.

  15. Modification of an HLA-B PCR-SSOP typing system leading to improved allele determination.

    Science.gov (United States)

    Middleton, D; Williams, F; Cullen, C; Mallon, E

    1995-04-01

    Modifications have been introduced to a previously reported HLA-B PCR-SSOP typing system. This has enabled further definition of alleles, determination of the probe pattern of some alleles not previously examined and identification of patterns of possible new alleles. However there are still some alleles that cannot be differentiated and there are several alleles which when present as a homozygote have the same pattern as in combination with another allele. When the method was applied to the typing of 66 consecutive cadaveric donors there were three donors whose type differed from the serological type.

  16. Development of an Intelligent System of Determinating the Coordinates and the Speed of the Train

    Directory of Open Access Journals (Sweden)

    Tarasov Evgenii M.

    2016-06-01

    Full Text Available Dynamic development of the country’s transport system leads to the increase of the length of highways, traffic interchange, including places of crossing with the railway. Notification time for crossing is determined by the maximum speed of the train, which is a significant disadvantage of the automatic crossing signaling. In reality the train speed is less than the estimated one, so the idles at transport intersection (crossing reach 30-30 minutes, creating not only inconveniences to vehicle traffic, but also unfavorable environmental conditions.

  17. Biomolecular Analysis Capability for Cellular and Omics Research on the International Space Station

    Science.gov (United States)

    Guinart-Ramirez, Y.; Cooley, V. M.; Love, J. E.

    2016-01-01

    International Space Station (ISS) assembly complete ushered a new era focused on utilization of this state-of-the-art orbiting laboratory to advance science and technology research in a wide array of disciplines, with benefits to Earth and space exploration. ISS enabling capability for research in cellular and molecular biology includes equipment for in situ, on-orbit analysis of biomolecules. Applications of this growing capability range from biomedicine and biotechnology to the emerging field of Omics. For example, Biomolecule Sequencer is a space-based miniature DNA sequencer that provides nucleotide sequence data for entire samples, which may be used for purposes such as microorganism identification and astrobiology. It complements the use of WetLab-2 SmartCycler"TradeMark", which extracts RNA and provides real-time quantitative gene expression data analysis from biospecimens sampled or cultured onboard the ISS, for downlink to ground investigators, with applications ranging from clinical tissue evaluation to multigenerational assessment of organismal alterations. And the Genes in Space-1 investigation, aimed at examining epigenetic changes, employs polymerase chain reaction to detect immune system alterations. In addition, an increasing assortment of tools to visualize the subcellular distribution of tagged macromolecules is becoming available onboard the ISS. For instance, the NASA LMM (Light Microscopy Module) is a flexible light microscopy imaging facility that enables imaging of physical and biological microscopic phenomena in microgravity. Another light microscopy system modified for use in space to image life sciences payloads is initially used by the Heart Cells investigation ("Effects of Microgravity on Stem Cell-Derived Cardiomyocytes for Human Cardiovascular Disease Modeling and Drug Discovery"). Also, the JAXA Microscope system can perform remotely controllable light, phase-contrast, and fluorescent observations. And upcoming confocal microscopy

  18. Method and system for fiber optic determination of gas concentrations in liquid receptacles

    Science.gov (United States)

    Nguyen, Quang-Viet (Inventor)

    2008-01-01

    A system for determining gas compositions includes a probe, inserted into a source of gaseous material, the probe having a gas permeable sensor tip and being capable of sending and receiving light to and from the gaseous material, a sensor body, connected to the probe, situated outside of the source and a fiber bundle, connected to the sensor body and communicating light to and from the probe. The system also includes a laser source, connected to one portion of the fiber bundle and providing laser light to the fiber bundle and the probe a Raman spectrograph, connected to another portion of the fiber bundle, receiving light from the probe and filtering the received light into specific channels and a data processing unit, receiving and analyzing the received light in the specific channels and outputting concentration of specific gas species in the gaseous material based on the analyzed received light.

  19. Determination of isothermal section of Ag-Ti-Zr ternary system at 1 023 K

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The isothermal section of Ag-Ti-Zr ternary system at 1023 K was determined by diffusion triple and electron probe microanalysis. The results indicate that four binary intermetallic phases of AgTi, AgTi2, AgZr and AgZr2 are found in Ag-Ti-Zr ternary system at 1 023 K. AgZr2 and AgTi2 form a continuous solid solution, namely Ag(Ti,Zr)2. Four three-phase regions: AgTi+AgZr + Ag, AgTi +AgZr + Ag (Ti, Zr)2, α-Zr +β3(Ti, Zr)+ Ag (Ti, Zr)2 and α-Ti +β(Ti, Zr)+ Ag (Ti, Zr)2 exist in the isothermal section. No ternary compound is observed.

  20. Novel approach for determining the optimal axial preload of a simulating rotary table spindle system

    Institute of Scientific and Technical Information of China (English)

    SHAN Xiao-biao; XIE Tao; CHEN Wei-shan

    2007-01-01

    This paper presents a new theoretical model to determine the optimal axial preload ora spindle system, for challenging the traditional method which relies heavily on experience of engineers. The axial preloading stiffness was treated as the sum of the spindle modal stiffness and the framework elastic stiffness, based on a novel concept that magnitude of preloads can be controlled by measuring the resonant frequency of a spindle system. By employing an example of a certain type of aircraft simulating rotary table, the modal stiffness was measured on the Agilent 35670A Dynamic Signal Analyzer by experimental modal analysis. The equivalent elastic stiffness was simulated by both finite element analysis in ANSYS(R) and a curve fitting in MATLAB(R). Results showed that the static preloading stiffness of the spindle was 7.2125×107 N/m, and that the optimal preloading force was 120.0848 N. Practical application proved the feasibility of our method.

  1. [Sensitive determination of Bi3+ by spectrofluorimetry based on graphene oxide-methylene blue system].

    Science.gov (United States)

    Zhai, Qiu-ge; Guo, Peng; Zhou, Lin; Liu, Yan-ming

    2014-08-01

    Graphene oxide was prepared by the modified Hummers method and characterized by field emission scanning electron microscopy. The interaction of graphene with methylene blue was studied by UV absorption, the intensity of two main absorption peaks of methylene blue decreased significantly after the fluorescence was quenched, and the energy transfer didn't occur because the overlap of the absorption spectrum of GO and the emission spectrum of MB is too small. Therefore, the fluorescence quenching of MB and GO was static. When adding a certain amount of Bi3+ in the graphene-methylene blue system, Bi3+ replaces the methylene blue from the graphene-methylene blue complexes because Bi3+ has the smaller volume and is more positively charged. The methylene blue therefore dissociates from the GO-MB complexes, resulting in the recovery of fluorescence of the system. Furthermore, the fluorescence of the system increases with the increase in the amount of Bi3+ due to the enhanced amount of MB in the system. A novel spectrofluorimetric method was therefore developed for the sensitive determination of Bi3+. Some parameters including the concentration of methylene blue, the amount of graphene oxide, the amount of nitric acid and the sequence of reagent adding were optimized to obtain higher sensitivity. The fluorescence of the system was detected at an emission wavelength of 667 nm with excitation at 690 nm. Under the optimized conditions, the concentration of Bi3+ showed good linear relationships with the fluorescence intensity in the range of 0.5-100 micromol x L(-1), with correlation coefficients of r = 0.9955. The limits of detection for Bi3+ was 1.0 x 10(-8) mol x L(-1) (S/N=3). The selectivity of the proposed method was evaluated and the results showed that 1000-fold K+, Ca+, Na+, Mg2+, Cu2+; 100-fold Fe3+, Be2+, SiO2- Al3+, Ni2+, Sb3+, NO3-, Cl-, F-, and 20-fold Pb2+, Hg2+, Cd2+ had negligible interference with the determination of Bi3+. The method has advantages of

  2. Determinants of performance of health systems concerning maternal and child health: a global approach.

    Directory of Open Access Journals (Sweden)

    Carlos Eduardo Pinzón-Flórez

    Full Text Available To assess the association of social determinants on the performance of health systems around the world.A transnational ecological study was conducted with an observation level focused on the country. In order to research on the strength of the association between the annual maternal and child mortality in 154 countries and social determinants: corruption, democratization, income inequality and cultural fragmentation, we used a mixed linear regression model for repeated measures with random intercepts and a conglomerate-based geographical analysis, between 2000 and 2010.Health determinants with a significant association on child mortality(<1year: higher access to water (βa Quartile 4(Q4 vs Quartile 1(Q1 = -6,14; 95%CI: -11,63 to -0,73, sanitation systems, (Q4 vs Q1 = -25,58; 95%CI: -31,91 to -19,25, % measles vaccination coverage (Q4 vs Q1 = -7.35; 95%CI: -10,18 to -4,52, % of births attended by a healthcare professional (Q4 vs Q1 = -7,91; 95%CI: -11,36 to -4,52 and a % of the total health expenditure (Q3 vs Q1 = -2,85; 95%CI: -4,93 to -0,7. Ethnic fragmentation (Q4 vs Q1 = 9,93; 95%CI: -0.03 to 19.89 had a marginal effect. For child mortality<5 years, an association was found for these variables and democratization (not free vs free = 11,23; 95%CI: -0,82 to 23,29, out-of-pocket expenditure (Q1 vs Q4 = 17,71; 95%CI: 5,86 to 29,56. For MMR (Maternal mortality ratio, % of access to water for all the quartiles, % of access to sanitation systems, (Q3 vs Q1 = -171,15; 95%CI: -281,29 to -61, birth attention by a healthcare professional (Q4 vs Q1 = -231,23; 95%CI: -349,32 to -113,15, and having corrupt government (Q3 vs Q1 = 83,05; 95%CI: 33,10 to 133.Improving access to water and sanitation systems, decreasing corruption in the health sector must become priorities in health systems. The ethno-linguistic cultural fragmentation and the detriment of democracy turn out to be two factors related to health results.

  3. Determinants of Performance of Health Systems Concerning Maternal and Child Health: A Global Approach

    Science.gov (United States)

    Pinzón-Flórez, Carlos Eduardo; Fernández-Niño, Julián Alfredo; Ruiz-Rodríguez, Myriam; Idrovo, Álvaro J.; Arredondo López, Abel Armando

    2015-01-01

    Aims To assess the association of social determinants on the performance of health systems around the world. Methods A transnational ecological study was conducted with an observation level focused on the country. In order to research on the strength of the association between the annual maternal and child mortality in 154 countries and social determinants: corruption, democratization, income inequality and cultural fragmentation, we used a mixed linear regression model for repeated measures with random intercepts and a conglomerate-based geographical analysis, between 2000 and 2010. Results Health determinants with a significant association on child mortality(<1year): higher access to water (βa Quartile 4(Q4) vs Quartile 1(Q1) = -6,14; 95%CI: -11,63 to -0,73), sanitation systems, (Q4 vs Q1 = -25,58; 95%CI: -31,91 to -19,25), % measles vaccination coverage (Q4 vs Q1 = -7.35; 95%CI: -10,18 to -4,52), % of births attended by a healthcare professional (Q4 vs Q1 = -7,91; 95%CI: -11,36 to -4,52) and a % of the total health expenditure (Q3 vs Q1 = -2,85; 95%CI: -4,93 to -0,7). Ethnic fragmentation (Q4 vs Q1 = 9,93; 95%CI: -0.03 to 19.89) had a marginal effect. For child mortality<5 years, an association was found for these variables and democratization (not free vs free = 11,23; 95%CI: -0,82 to 23,29), out-of-pocket expenditure (Q1 vs Q4 = 17,71; 95%CI: 5,86 to 29,56). For MMR (Maternal mortality ratio), % of access to water for all the quartiles, % of access to sanitation systems, (Q3 vs Q1 = -171,15; 95%CI: -281,29 to -61), birth attention by a healthcare professional (Q4 vs Q1 = -231,23; 95%CI: -349,32 to -113,15), and having corrupt government (Q3 vs Q1 = 83,05; 95%CI: 33,10 to 133). Conclusions Improving access to water and sanitation systems, decreasing corruption in the health sector must become priorities in health systems. The ethno-linguistic cultural fragmentation and the detriment of democracy turn out to be two factors related to health results. PMID

  4. Molecular features determining different partitioning patterns of papain and bromelain in aqueous two-phase systems.

    Science.gov (United States)

    Rocha, Maria Victoria; Nerli, Bibiana Beatriz

    2013-10-01

    The partitioning patterns of papain (PAP) and bromelain (BR), two well-known cysteine-proteases, in polyethyleneglycol/sodium citrate aqueous two-phase systems (ATPSs) were determined. Polyethyleneglycols of different molecular weight (600, 1000, 2000, 4600 and 8000) were assayed. Thermodynamic characterization of partitioning process, spectroscopy measurements and computational calculations of protein surface properties were also carried out in order to explain their differential partitioning behavior. PAP was observed to be displaced to the salt-enriched phase in all the assayed systems with partition coefficients (KpPAP) values between 0.2 and 0.9, while BR exhibited a high affinity for the polymer phase in systems formed by PEGs of low molecular weight (600 and 1000) with partition coefficients (KpBR) values close to 3. KpBR values resulted higher than KpPAP in all the cases. This difference could be assigned neither to the charge nor to the size of the partitioned biomolecules since PAP and BR possess similar molecular weight (23,000) and isoelectric point (9.60). The presence of highly exposed tryptophans and positively charged residues (Lys, Arg and His) in BR molecule would be responsible for a charge transfer interaction between PEG and the protein and, therefore, the uneven distribution of BR in these systems.

  5. Consequences of respiration in the light on the determination of production in pelagic systems

    Directory of Open Access Journals (Sweden)

    O. Pringault

    2007-01-01

    Full Text Available Oxygen microprobes were used to estimate Community Respiration (R, Net Community Production (NCP and Gross Primary Production (GPP in coastal seawater samples. Using this highly stable and reproducible technique to measure oxygen change during alternating dark and light periods, we show that respiration in the light could account for up to 640% of respiration in the dark. The light enhanced dark respiration can remain elevated for several hours following a 12 h period of illumination. Not including Rlight into calculations of production leads to an underestimation of GPP, which can reach up to 650% in net heterotrophic systems. The production: respiration (P:R ratio is in turn affected by the higher respiration rates and by the underestimation of GPP. While the integration of Rlight into the calculation of P:R ratio does not change the metabolic balance of the system, it decreases the observed tendency, thus net autotrophic systems become less autotrophic and net heterotrophic systems become less heterotrophic. As a consequence, we propose that efforts have to be focused on the estimation and the integration of Rlight into the determination of GPP and R for a better understanding of the aquatic carbon cycle.

  6. Asteroseismic determination of obliquities of the exoplanet systems Kepler-50 and Kepler-65

    CERN Document Server

    Chaplin, W J; Campante, T L; Handberg, R; Stello, D; Winn, J N; Basu, S; Christensen-Dalsgaard, J; Davies, G R; Metcalfe, T S; Buchhave, L A; Fischer, D A; Bedding, T R; Cochran, W D; Elsworth, Y; Gilliland, R L; Hekker, S; Huber, D; Isaacson, H; Karoff, C; Kawaler, S D; Kjeldsen, H; Latham, D W; Lund, M N; Lundkvist, M; Marcy, G W; Miglio, A; Barclay, T; Lissauer, J J

    2013-01-01

    Results on the obliquity of exoplanet host stars -- the angle between the stellar spin axis and the planetary orbital axis -- provide important diagnostic information for theories describing planetary formation. Here we present the first application of asteroseismology to the problem of stellar obliquity determination in systems with transiting planets and Sun-like host stars. We consider two systems observed by the NASA Kepler Mission which have multiple transiting small (super-Earth sized) planets: the previously reported Kepler-50 and a new system, Kepler-65, whose planets we validate in this paper. Both stars show rich spectra of solar-like oscillations. From the asteroseismic analysis we find that each host has its rotation axis nearly perpendicular to the line of sight with the sines of the angles constrained at the 1-sigma level to lie above 0.97 and 0.91, respectively. We use statistical arguments to show that coplanar orbits are favoured in both systems, and that the orientations of the planetary orb...

  7. ASTEROSEISMIC DETERMINATION OF OBLIQUITIES OF THE EXOPLANET SYSTEMS KEPLER-50 AND KEPLER-65

    Energy Technology Data Exchange (ETDEWEB)

    Chaplin, W. J.; Campante, T. L.; Davies, G. R.; Elsworth, Y.; Hekker, S. [School of Physics and Astronomy, University of Birmingham, Edgbaston, Birmingham B15 2TT (United Kingdom); Sanchis-Ojeda, R.; Winn, J. N. [Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 (United States); Handberg, R.; Christensen-Dalsgaard, J.; Karoff, C. [Stellar Astrophysics Centre (SAC), Department of Physics and Astronomy, Aarhus University, Ny Munkegade 120, DK-8000 Aarhus C (Denmark); Stello, D.; Bedding, T. R. [Sydney Institute for Astronomy, School of Physics, University of Sydney, Sydney (Australia); Basu, S.; Fischer, D. A. [Department and Astronomy, Yale University, New Haven, CT 06520 (United States); Metcalfe, T. S. [White Dwarf Research Corporation, Boulder, CO 80301 (United States); Buchhave, L. A. [Niels Bohr Institute, Copenhagen University, DK-2100 Copenhagen (Denmark); Cochran, W. D. [McDonald Observatory, The University of Texas, Austin, TX 78712 (United States); Gilliland, R. L. [Center for Exoplanets and Habitable Worlds, The Pennsylvania State University, University Park, PA 16802 (United States); Huber, D. [NASA Ames Research Center, MS 244-30, Moffett Field, CA 94035 (United States); Isaacson, H. [Department of Astronomy, University of California, Berkeley, CA 94720 (United States); and others

    2013-04-01

    Results on the obliquity of exoplanet host stars-the angle between the stellar spin axis and the planetary orbital axis-provide important diagnostic information for theories describing planetary formation. Here we present the first application of asteroseismology to the problem of stellar obliquity determination in systems with transiting planets and Sun-like host stars. We consider two systems observed by the NASA Kepler mission which have multiple transiting small (super-Earth sized) planets: the previously reported Kepler-50 and a new system, Kepler-65, whose planets we validate in this paper. Both stars show rich spectra of solar-like oscillations. From the asteroseismic analysis we find that each host has its rotation axis nearly perpendicular to the line of sight with the sines of the angles constrained at the 1{sigma} level to lie above 0.97 and 0.91, respectively. We use statistical arguments to show that coplanar orbits are favored in both systems, and that the orientations of the planetary orbits and the stellar rotation axis are correlated.

  8. Calibration of dual-energy gamma systems for determining liquid saturations during multiphase flow in soil

    Energy Technology Data Exchange (ETDEWEB)

    Bali, K.M.; Grismer, M.E. [University of California, Cooperative Extension and University of California, Holtville (United States)

    1994-12-31

    The purpose of this study was to calibrate a dual-energy gamma system for simultaneous determination of aqueous and non-aqueous phase liquid (NAPL) in soil column. A dual energy gamma system containing {sup 241}Am and {sup 137}Cs was used to study the infiltration and displacement of aqueous liquid by NAPL and vice versa. Distilled water and Nal solution, and Soltrol 130 were used as fluids. The system was calibrated to minimize errors in liquid saturations due to random nature of gamma photons emission and drift in the photon detection equipment. The measurement accuracy in liquid saturations was substantially improved by increasing counting time and fluid attenuation coefficient. Nal salt was used to increase the attenuation coefficient of water. Measured and predicted liquid saturation during immiscible displacement in soil were consistent with mass balance measurements and anticipated deviations in saturations from probable error calculations. The calibration procedure resulted in a significant improvement in the prediction of liquid saturation using dual-energy gamma system. (author). 8 refs, 4 tabs.

  9. Ecological determinants of mating system within and between three Fagus sylvatica populations along an elevational gradient.

    Science.gov (United States)

    Gauzere, Julie; Klein, Etienne K; Oddou-Muratorio, Sylvie

    2013-10-01

    Studies addressing the variation of mating system between plant populations rarely account for the variability of these parameters between individuals within populations, although this variability is often non-negligible. Here, we propose a new direct method based on paternity analyses (Mixed Effect Mating Model) to estimate individual migration (mi ) and selfing rates (si ) together with the pollen dispersal kernel. Using this method and the KINDIST approach, we investigated the variation of mating system parameters within and between three populations of Fagus sylvatica along an elevational gradient. Among the mother trees, si varied from 0% to 48%, mi varied from 12% to 86% and the effective number of pollen donors (Nepi ) varied from 2 to 364. The mating patterns differed along the gradient, the top population showing higher m and lower s, and a trend to higher Nep than the bottom populations. The phenological lag shaped long-distance pollen flow both within population (by increasing mi at mother-tree level) and between populations (by increasing m at high elevation). Rather than the mate density, the canopy density was detected as a major mating system determinant within population; it acted as a barrier to pollen flow, decreasing the proportion of long-distance pollen flow and increasing si . Overall, the effects of ecological factors on mating system were not the same within vs. between populations across the gradient, and these factors also differed from those traditionally found to shape variation at range-wide scale, highlighting the interest of multiscale approaches.

  10. Spectrophotometric high-precision seawater pH determination for use in underway measuring systems

    Science.gov (United States)

    Aßmann, S.; Frank, C.; Körtzinger, A.

    2011-10-01

    Autonomous sensors are required for a comprehensive documentation of the changes in the marine carbon system and thus to differentiate between its natural variability and anthropogenic impacts. Spectrophotometric determination of pH - a key variable of the seawater carbon system - is particularly suited to achieve precise and drift-free measurements. However, available spectrophotometric instruments are not suitable for integration into automated measurement systems (e.g. FerryBox) since they do not meet the major requirements of reliability, stability, robustness and moderate cost. Here we report on the development and testing of a~new indicator-based pH sensor that meets all of these requirements. This sensor can withstand the rough conditions during long-term deployments on ships of opportunity and is applicable to the open ocean as well as to coastal waters with a complex matrix and highly variable conditions. The sensor uses a high resolution CCD spectrometer as detector connected via optical fibers to a custom-made cuvette designed to reduce the impact of air bubbles. The sample temperature can be precisely adjusted (25 °C ± 0.006 °C) using computer-controlled power supplies and Peltier elements thus avoiding the widely used water bath. The overall setup achieves a measurement frequency of 1 min-1 with a precision of ±0.0007 pH units, an average offset of +0.0005 pH units to a reference system, and an offset of +0.0081 pH units to a certified standard buffer. Application of this sensor allows monitoring of seawater pH in autonomous underway systems, providing a key variable for characterization and understanding of the marine carbon system.

  11. Spectrophotometric high-precision seawater pH determination for use in underway measuring systems

    Directory of Open Access Journals (Sweden)

    S. Aßmann

    2011-10-01

    Full Text Available Autonomous sensors are required for a comprehensive documentation of the changes in the marine carbon system and thus to differentiate between its natural variability and anthropogenic impacts. Spectrophotometric determination of pH – a key variable of the seawater carbon system – is particularly suited to achieve precise and drift-free measurements. However, available spectrophotometric instruments are not suitable for integration into automated measurement systems (e.g. FerryBox since they do not meet the major requirements of reliability, stability, robustness and moderate cost. Here we report on the development and testing of a~new indicator-based pH sensor that meets all of these requirements. This sensor can withstand the rough conditions during long-term deployments on ships of opportunity and is applicable to the open ocean as well as to coastal waters with a complex matrix and highly variable conditions. The sensor uses a high resolution CCD spectrometer as detector connected via optical fibers to a custom-made cuvette designed to reduce the impact of air bubbles. The sample temperature can be precisely adjusted (25 °C ± 0.006 °C using computer-controlled power supplies and Peltier elements thus avoiding the widely used water bath. The overall setup achieves a measurement frequency of 1 min−1 with a precision of ±0.0007 pH units, an average offset of +0.0005 pH units to a reference system, and an offset of +0.0081 pH units to a certified standard buffer. Application of this sensor allows monitoring of seawater pH in autonomous underway systems, providing a key variable for characterization and understanding of the marine carbon system.

  12. A new state of charge determination method for battery management system

    Institute of Scientific and Technical Information of China (English)

    ZHU Chun-bo 朱春波; WANG Tie-cheng 王铁成; HURLEY W G

    2004-01-01

    State of Charge (SOC) determination is an increasingly important issue in battery technology. In addition to the immediate display of the remaining battery capacity to the user, precise knowledge of SOC exerts additional control over the charging/discharging process which in turn reduces the risk of over-voltage and gassing, which degrade the chemical composition of the electrolyte and plates. This paper describes a new approach to SOC determination for the lead-acid battery management system by combining Ah-balance with an EMF estimation algorithm, which predicts the battery' s EMF value while it is under load. The EMF estimation algorithm is based on an equivalent-circuit representation of the battery, with the parameters determined from a pulse test performed on the battery and a curve-fitting algorithm by means of least-square regression. The whole battery cycle is classified into seven states where the SOC is estimated with the Ah-balance method and the proposed EMF based algorithm. Laboratory tests and results are described in detail in the paper.

  13. Determination of Biotin in Pharmaceutical Formulations by Potassium Permanganate-luminol-CdTe Nanoparticles Chemiluminescence System

    Institute of Scientific and Technical Information of China (English)

    TRAORE Zoumana Sékou; SU Xing-guang

    2012-01-01

    A sensitive flow-injection chemiluminescence method was developed for the determination of biotin in the pharmaceutical formulations.The affinity between avidin and biotin was used to adsorb biotin on the polystyrene,with subsequent quantification of biotin based on its ability to enhance the chemiluminescence(CL) signal generated by the redox reaction of potassium permanganate-luminol-CdTe nanoparticles CL system.The investigations prove that apart from 3-aminophthalate,the CdTe quantum dots(QDs) play both catalytic and emitter roles.Under optimum conditions,the linear range for the determination of biotin was 0.01-25 ng/mL with a detection limit of 7.3×10-3ng/mL(S/N=3).The relative standard deviation of 5 ng/L biotin was 2.06%(n=7).The proposed method was used to determine the biotin concentration in the pharmaceutical formulations and the recovery was between 96.4% and 104%.The proposed method is simple,convenient,rapid and sensitive.

  14. Determination of epinephrine by the Briggs-Rauscher oscillating system using non-equilibrium stationary state

    Directory of Open Access Journals (Sweden)

    Gao Jinzhang

    2012-01-01

    Full Text Available A highly sensitive method for the determination of epinephrine was proposed, which was based on the perturbation of epinephrine to Briggs-Rauscher oscillating system involving malonic acid, Mn2+, H+, IO3 - and H2O2 at non-equilibrium stationary state. The concentration of KIO3 was chosen as a control parameter to find the bifurcation point in this paper. Results showed that a well linear relationship between the difference of potential and the negative logarithm concentrations of epinephrine existed in the range of 1.1×10-7~5.2×10-9 mol L-1 with a lower detection limit of 6.8×10-10mol L-1 and a correlation coefficient of 0.9974. Compared to the classical oscillating reaction, this method has a lower detection limit and wider linear range. The effects of some foreign species, which may possibly be existed with epinephrine, on determination were also investigated. The proposed method has been successfully used to determine the epinephrine both in the serum and adrenaline hydrochloride injection.

  15. Preconcentration system for cadmium and lead determination in environmental samples using polyurethane foam/Me-BTANC

    Energy Technology Data Exchange (ETDEWEB)

    Moreira Gama, Ednilton [Universidade Estadual do Sudoeste da Bahia, Nucleo de Quimica Analitica da Bahia (NQA), Laboratorio de Quimica Analitica (LQA), Campus de Jequie 45200-000, Jequie-BA (Brazil); Silva Lima, Adriana da [Universidade Estadual do Sudoeste da Bahia, Nucleo de Quimica Analitica da Bahia (NQA), Laboratorio de Quimica Analitica (LQA), Campus de Jequie 45200-000, Jequie-BA (Brazil); Azevedo Lemos, Valfredo [Universidade Estadual do Sudoeste da Bahia, Nucleo de Quimica Analitica da Bahia (NQA), Laboratorio de Quimica Analitica (LQA), Campus de Jequie 45200-000, Jequie-BA (Brazil)]. E-mail: vlemos@uesb.br

    2006-08-25

    In this work, polyurethane foam (PUF) loaded with 2-(6'-methyl-2'-benzothiazolylazo)chromotropic acid (Me-BTANC) was packed in a minicolumn and it was used in an on-line preconcentration system for cadmium and lead determination. Optimum hydrodynamic and chemical conditions for metal sorption were investigated. The effects of several foreign substances on the adsorption of cadmium and lead were also reported. The enrichment factor obtained was 37 (Cd and Pb) for 180 s preconcentration time. The proposed procedures allowed the determination of metals with detection limits (3{sigma}) of 0.80 and 3.75 {mu}g L{sup -1} (0.10 and 0.47 {mu}g g{sup -1} of solid sample) for cadmium and lead, respectively. The precision of the procedures was also calculated: 3.1 (Cd 10 {mu}g L{sup -1}) and 4.4% (Pb 100 {mu}g L{sup -1}). The accuracy of the procedure was checked by analysis of the certified reference materials Spinach Leaves and Fish Tissue. Cadmium and lead contents in environmental samples (black tea, spinach leaves, natural and tap water) were determined by applying the proposed procedure.

  16. A Statistical Methodology for Determination of Safety Systems Actuation Setpoints Based on Extreme Value Statistics

    Directory of Open Access Journals (Sweden)

    D. R. Novog

    2008-01-01

    Full Text Available This paper provides a novel and robust methodology for determination of nuclear reactor trip setpoints which accounts for uncertainties in input parameters and models, as well as accounting for the variations in operating states that periodically occur. Further it demonstrates that in performing best estimate and uncertainty calculations, it is critical to consider the impact of all fuel channels and instrumentation in the integration of these uncertainties in setpoint determination. This methodology is based on the concept of a true trip setpoint, which is the reactor setpoint that would be required in an ideal situation where all key inputs and plant responses were known, such that during the accident sequence a reactor shutdown will occur which just prevents the acceptance criteria from being exceeded. Since this true value cannot be established, the uncertainties in plant simulations and plant measurements as well as operational variations which lead to time changes in the true value of initial conditions must be considered. This paper presents the general concept used to determine the actuation setpoints considering the uncertainties and changes in initial conditions, and allowing for safety systems instrumentation redundancy. The results demonstrate unique statistical behavior with respect to both fuel and instrumentation uncertainties which has not previously been investigated.

  17. [Establishment of culture system of Silybum marianum hairy roots and determination of silybin].

    Science.gov (United States)

    Zhang, Shu-Li; Zhang, Tian-Zhu; Yang, Shi-Hai

    2014-06-01

    This research uses six Agrobacterium rhizogenes R1601, R15384, R1000, A4, R1025 and R1 to infect silymarin explants to induce hairy roots and silibin. All of the six A. rhizogenes can induce Silybum marianum to generate hairy roots and the A. rhizogene A4 shows comparatively high infection on the plant. This research determines the condition to induce silymarin hairy roots by the factors of infection time, pre-culturing, co-culturing and pH value. The fact that MS liquid medium fits the proliferation of silymarin hairy roots is determined. Through PCR molecular identification, it can be seen that the DNA plasmids in the A. rhizogenes are successfully integrated into the genome of transformed roots. Using liquid chromatography, it is determined that the silibin content in silymarin hairy roots is 2.5 times that in the plant In this research, the silymarin hairy roots culturing system is established, which lays a foundation for the study of culturing silymarin hairy roots and producing silibin.

  18. A novel chemiluminescence reaction system for the determination of norfloxacin with Ag(III) complex

    Science.gov (United States)

    Sun, Hanwen; Chen, Peiyun; Wang, Fei

    2009-10-01

    A novel chemiluminescence (CL) system for the determination of norfloxacin (NFLX) is developed based on the direct CL reaction of [Ag(HIO 6) 2] 5--H 2SO 4-NFLX system. The possible mechanism of CL emission and enhancing effect was discussed by comparing UV, fluorescence and CL spectra. [Ag(HIO 6) 2] 5- in the presence of H 2SO 4 could produce CL emission at 490 nm, this might be caused by the excited state (O 2) 2*. The enhancing effect of NFLX may be produced through an intermolecular energy transfer from part of (O 2) 2* to NFLX molecule and complex of Ag 3+ and NFLX. The CL intensity emission intensity was linear in the range 1.34 × 10 -8 to 5.44 × 10 -6 g mL -1 with correlation coefficient of 0.9982. The detection limit (s/n = 3) was 3.10 × 10 -9 g mL -1. The recovery was in the range of 90.0-104% with the RSD of 1.1-2.8%. The proposed flow injection CL method was applied satisfactorily for the determination of NFLX in capsule, human serum and urine.

  19. A GPS based fawn saving system using relative distance and angle determination

    Science.gov (United States)

    Ascher, A.; Eberhardt, M.; Lehner, M.; Biebl, E.

    2016-09-01

    Active UHF RFID systems are often used for identifying, tracking and locating objects. In the present publication a GPS- based localization system for saving fawns during pasture mowing was introduced and tested. Fawns were first found by a UAV before mowing began. They were then tagged with small active RFID transponders, and an appropriate reader was installed on a mowing machine. Conventional direction-of-arrival approaches require a large antenna array with multiple elements and a corresponding coherent receiver, which introduces a large degree of complexity on the reader-side. Instead, our transponders were equipped with a small GPS module, allowing a transponder to determine its own position on request from the reader. A UHF link was used to transmit the location to a machine- mounted reader, where a second GPS receiver was installed. Using information from this second position and a machine- mounted magnetometer for determining the relative north direction of a vehicle, relative distance, and angle between GPS receivers can be calculated. The accuracy and reliability of this novel method were tested under realistic operating conditions, considering critical factors such as the height of grass, the lying position of a fawn, humidity and geographical area.

  20. Systemic arterial and venous determinants of renal hemodynamics in congestive heart failure.

    Science.gov (United States)

    Braam, Branko; Cupples, William A; Joles, Jaap A; Gaillard, Carlo

    2012-03-01

    Heart and kidney interactions are fascinating, in the sense that failure of the one organ strongly affects the function of the other. In this review paper, we analyze how principal driving forces for glomerular filtration and renal blood flow are changed in heart failure. Moreover, renal autoregulation and modulation of neurohumoral factors, which can both have repercussions on renal function, are analyzed. Two paradigms seem to apply. One is that the renin-angiotensin system (RAS), the sympathetic nervous system (SNS), and extracellular volume control are the three main determinants of renal function in heart failure. The other is that the classical paradigm to analyze renal dysfunction that is widely applied in nephrology also applies to the pathophysiology of heart failure: pre-renal, intra-renal, and post-renal alterations together determine glomerular filtration. At variance with the classical paradigm is that the most important post-renal factor in heart failure seems renal venous hypertension that, by increasing renal tubular pressure, decreases GFR. When different pharmacological strategies to inhibit the RAS and SNS and to assist renal volume control are considered, there is a painful lack in knowledge about how widely applied drugs affect primary driving forces for ultrafiltration, renal autoregulation, and neurohumoral control. We call for more clinical physiological studies.

  1. Photoelectrocatalytic determination of NADH in a flow injection system with electropolymerized methylene blue

    Energy Technology Data Exchange (ETDEWEB)

    Dilgin, Yusuf, E-mail: ydilgin@yahoo.co [Canakkale Onsekiz Mart University, Science and Art Faculty, Department of Chemistry, TR-17100 Canakkale (Turkey); Dilgin, Didem Giray [Canakkale Onsekiz Mart University, Biga Vocational College, TR-17200 Biga Canakkale (Turkey); Ege University, Science Faculty, Department of Chemistry, TR-35100 Bornova/Izmir (Turkey); Dursun, Zekerya; Goekcel, H. Ismet [Ege University, Science Faculty, Department of Chemistry, TR-35100 Bornova/Izmir (Turkey); Gligor, Delia [Department of Environmental Physics, Chemistry and Engineering, ' Babes-Bolyai' University, 30 Fantanele St., 400294 Cluj-Napoca (Romania); Bayrak, Burcu; Ertek, Bensu [Canakkale Onsekiz Mart University, Science and Art Faculty, Department of Chemistry, TR-17100 Canakkale (Turkey)

    2011-01-01

    It was firstly described that a glassy carbon electrode electropolymerized with methylene blue shows an efficient photoelectrocatalytic activity towards NADH oxidation in a phosphate buffer solution (pH 7.0). In order to perform the photoelectrocatalytic determination of NADH in a flow injection analysis (FIA) system, a home-made flow electrochemical cell with a suitable transparent window for the irradiation of the electrode surface was constructed. The currents obtained from the photoamperometric measurements in the FIA system at optimum conditions (flow rate of carrier solution, 1.3 mL min{sup -1}; transmission tubing length, 10 cm; injection volume, 100 {mu}L; and constant applied potential, +150 mV vs. Ag/AgCl) were linearly dependent on the NADH concentration and linear calibration curves were obtained in the range of 1.0 x 10{sup -7}-2.0 x 10{sup -4} M. The detection limit was found to be 4.0 x 10{sup -8} M for photoamperometric determination of NADH.

  2. Determination of optimal collimation parameters for a rotating slat collimator system: a system matrix method using ML-EM

    Science.gov (United States)

    Boisson, F.; Bekaert, V.; Brasse, D.

    2016-03-01

    Nowadays, Single Photon imaging has become an essential part of molecular imaging and nuclear medicine. Whether to establish a diagnosis or in the therapeutic monitoring, this modality presents performance that continues to improve. For over 50 years, several collimators have been proposed. Mainly governed by collimation parameters, the resolution-sensitivity trade-off is the factor determining the collimator the most suitable for an intended study. One alternative to the common approaches is the rotating slat collimator (RSC). In the present study, we are aiming at developing a preclinical system equipped with a RSC dedicated to mice and rats imaging, which requires both high sensitivity and spatial resolution. We investigated the resolution-sensitivity trade-offs obtained by varying different collimation parameters: (i) the slats height (H), and (ii) the gap between two consecutive slats (g), considering different intrinsic spatial resolutions. One system matrix was generated for each set of collimation parameters (H,g). Spatial resolutions, Signal-to-Noise Ratio (SNR) and sensitivity obtained for all the set of collimation parameters (H,g) were measured in the 2D projections reconstructed with ML-EM. According to our results, 20 mm high slats and a 1 mm gap were chosen as a good RSC candidate for a preclinical detection module. This collimator will ensure a sensitivity greater than 0.2% and a system spatial resolution below 1 mm, considering an intrinsic spatial resolution below 0.8 mm.

  3. Determining of a robot workspace using the integration of a CAD system with a virtual control system

    Science.gov (United States)

    Herbuś, K.; Ociepka, P.

    2016-08-01

    The paper presents a method for determining the workspace of an industrial robot using an approach consisting in integration a 3D model of an industrial robot with a virtual control system. The robot model with his work environment, prepared for motion simulation, was created in the “Motion Simulation” module of the Siemens PLM NX software. In the mentioned model components of the “link” type were created which map the geometrical form of particular elements of the robot and the components of “joint” type mapping way of cooperation of components of the “link” type. In the paper is proposed the solution in which the control process of a virtual robot is similar to the control process of a real robot using the manual control panel (teach pendant). For this purpose, the control application “JOINT” was created, which provides the manipulation of a virtual robot in accordance with its internal control system. The set of procedures stored in an .xlsx file is the element integrating the 3D robot model working in the CAD/CAE class system with the elaborated control application.

  4. Noble metals determination in ancient jewels with portable ED-XRF system

    Energy Technology Data Exchange (ETDEWEB)

    Parreira, Paulo S.; Galvao, Tiago D.; Appoloni, Carlos R. [Universidade Estadual de Londrina (UEL), PR (Brazil). Dept. de Fisica. Lab. de Fisica Nuclear Aplicada ], e-mail: parreira@uel.br, e-mail: tdggalvao@yahoo.com.br, e-mail: appoloni@uel.br

    2009-07-01

    A handmade system of Energy Dispersive X-Ray Fluorescence (ED-XRF) was used to perform the analysis of some jewels of the XIX century, as napkin holder, tobacco case, cigarette case, pen, pendant shrines, bracelets and a crucifix from the collection of the Museu Historico Nacional do Rio de Janeiro (MHN), Brazil. It was possible to verify the presence of Cu, Au and Ag as macro elements of the alloys, besides Hg as contaminant for one silver piece. Some gold and silver coins with well-known concentrations of gold and silver were also analysed, as reference material, to check out the methodology. To determine the concentrations of the metals, a methodology based on the equation of the fundamental parameters was used. For the jewels with silver aspect, it was possible to determine in average 90.4% of Ag for the napkin holder and 46.6% of Ag for one the bracelets, this last one presented also a high concentration of copper. For the jewels with golden aspect, it was possible to determine, in average, 88.6% to 98.9% for the Au content . For one special piece it was observed 62.5% of Au and 37.5% of Cu. For the coins, the obtained values showed a deviation of 0.4 and 7.6 percent for the average concentration of noble metals Ag and Au, respectively. The portable X-ray system showed to be a powerful tool in the investigation of metallic alloys with high concentration of major elements, allowing in situ measurements.(author)

  5. Fast Moment Magnitude Determination from P-wave Trains for Bucharest Rapid Early Warning System (BREWS)

    Science.gov (United States)

    Lizurek, Grzegorz; Marmureanu, Alexandru; Wiszniowski, Jan

    2017-03-01

    Bucharest, with a population of approximately 2 million people, has suffered damage from earthquakes in the Vrancea seismic zone, which is located about 170 km from Bucharest, at a depth of 80-200 km. Consequently, an earthquake early warning system (Bucharest Rapid earthquake Early Warning System or BREWS) was constructed to provide some warning about impending shaking from large earthquakes in the Vrancea zone. In order to provide quick estimates of magnitude, seismic moment was first determined from P-waves and then a moment magnitude was determined from the moment. However, this magnitude may not be consistent with previous estimates of magnitude from the Romanian Seismic Network. This paper introduces the algorithm using P-wave spectral levels and compares them with catalog estimates. The testing procedure used waveforms from about 90 events with catalog magnitudes from 3.5 to 5.4. Corrections to the P-wave determined magnitudes according to dominant intermediate depth events mechanism were tested for November 22, 2014, M5.6 and October 17, M6 events. The corrections worked well, but unveiled overestimation of the average magnitude result of about 0.2 magnitude unit in the case of shallow depth event ( H < 60 km). The P-wave spectral approach allows for the relatively fast estimates of magnitude for use in BREWS. The average correction taking into account the most common focal mechanism for radiation pattern coefficient may lead to overestimation of the magnitude for shallow events of about 0.2 magnitude unit. However, in case of events of intermediate depth of M6 the resulting M w is underestimated at about 0.1-0.2. We conclude that our P-wave spectral approach is sufficiently robust for the needs of BREWS for both shallow and intermediate depth events.

  6. Determination of the kinetic rate constant of cyclodextrin supramolecular systems by high performance affinity chromatography.

    Science.gov (United States)

    Li, Haiyan; Ge, Jingwen; Guo, Tao; Yang, Shuo; He, Zhonggui; York, Peter; Sun, Lixin; Xu, Xu; Zhang, Jiwen

    2013-08-30

    It is challenging and extremely difficult to measure the kinetics of supramolecular systems with extensive, weak binding (Kahigh performance affinity chromatography (HPAC) was established to determine the dissociation rate constant of cyclodextrin supramolecular systems. The interactions of β-cyclodextrin with acetaminophen and sertraline were used to exemplify the method. The retention times, variances and the plate heights of the peaks for acetaminophen or sertraline, conventional non-retained substance (H2O) on the β-cyclodextrin bonded column and a control column were determined at four flow rates under linear elution conditions. Then, plate heights for the theoretical non-retained substance were estimated by the modified HPAC method, in consideration of the diffusion and stagnant mobile phase mass transfer. As a result, apparent dissociation rate constants of 1.82 (±0.01)s(-1) and 3.55 (±0.37)s(-1) were estimated for acetaminophen and sertraline respectively at pH 6.8 and 25°C with multiple flow rates. Following subtraction of the non-specific binding with the support, dissociation rate constants were estimated as 1.78 (±0.00) and 1.91 (±0.02)s(-1) for acetaminophen and sertraline, respectively. These results for acetaminophen and sertraline were in good agreement with the magnitude of the rate constants for other drugs determined by capillary electrophoresis reported in the literature and the peak fitting method we performed. The method described in this work is thought to be suitable for other supramolecules, with relatively weak, fast and extensive interactions.

  7. Determination of the thermodynamic properties of liquid Ag-Sb-Sn system by equilibrium saturation method

    Directory of Open Access Journals (Sweden)

    J. Romanowska

    2011-09-01

    Full Text Available Purpose: The interaction of lead-free solders with a copper substrate is an essential issue for the reliability of solder joints. In order to understand this interaction, the knowledge of thermodynamic and other physical properties of several ternary systems such as Ag-Sb-Sn system is necessary. The aim of this work was to determine the activities of all components in Ag-Sb-Sn alloy.Design/methodology/approach: The investigation of this system was carried out using the equilibrium saturation (ES method. The ES measurements were performed at 1273, 1373 and 1473 K. As the latter method is a comparative one, a Sn-Sb alloy was accepted as a reference alloy, where a formula for the Sb activity proposed by Jönsson and verified by Vassiliev was accepted.Findings: In the frame of the presented experiments the activity of Sb was determined by ES method.Research limitations/implications: The activity of Sb was obtained by ES and fitted to the Redlich-Kister-Muggianu (RKM model.Practical implications: A knowledge of multi-component phase equilibrium can provide the alloy developer with specific data enabling finding alloys that meet certain criteria. Phase diagrams are built on the basis of experimental data and the reliability of phase diagrams depends on the reliability of the experimental data used for the optimisation. Hence it is advantageous to use various source of data obtained by several methods and when the data of different source agree (like the ones presented in this paper it proves their reliability. Data presented in this paper will be used for Ag-Sb-Sn phase diagram optimisation in the frame of the COST Action MP0602.Originality/value: Sb activity values in Ag-Sb-Sn alloys obtained by ES and activity values of Sb, Ag and Sn calculated using the RKM model.

  8. Determining airborne concentrations of spatial repellent chemicals in mosquito behavior assay systems.

    Directory of Open Access Journals (Sweden)

    Nicholas J Martin

    Full Text Available BACKGROUND: Mosquito behavior assays have been used to evaluate the efficacy of vector control interventions to include spatial repellents (SR. Current analytical methods are not optimized to determine short duration concentrations of SR active ingredients (AI in air spaces during entomological evaluations. The aim of this study was to expand on our previous research to further validate a novel air sampling method to detect and quantitate airborne concentrations of a SR under laboratory and field conditions. METHODOLOGY/PRINCIPAL FINDINGS: A thermal desorption (TD gas chromatography-mass spectrometry (GC-MS method was used to determine the amount of dichlorodiphenyltrichloroethane (DDT in samples of air. During laboratory experiments, 1 L volumes of air were collected over 10 min intervals from a three-chamber mosquito behavior assay system. Significantly higher levels of airborne DDT were measured in the chamber containing textiles treated with DDT compared to chambers free of AI. In the field, 57 samples of air were collected from experimental huts with and without DDT for onsite analysis. Airborne DDT was detected in samples collected from treated huts. The mean DDT air concentrations in these two huts over a period of four days with variable ambient temperature were 0.74 µg/m(3 (n = 17; SD = 0.45 and 1.42 µg/m(3 (n = 30; SD = 0.96. CONCLUSIONS/SIGNIFICANCE: The results from laboratory experiments confirmed that significantly different DDT exposure conditions existed in the three-chamber system establishing a chemical gradient to evaluate mosquito deterrency. The TD GC-MS method addresses a need to measure short-term (<1 h SR concentrations in small volume (<100 L samples of air and should be considered for standard evaluation of airborne AI levels in mosquito behavior assay systems. Future studies include the use of TD GC-MS to measure other semi-volatile vector control compounds.

  9. Single x-ray transmission system for bone mineral density determination

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez-Mendoza, Daniel; Vargas-Vazquez, Damian [Division de Investigacion y Posgrado, Facultad de Ingenieria, Universidad Autonoma de Queretaro, Cerro de las Campanas s/n., C.P. 76010, Queretaro, Qro. (Mexico); Espinosa-Arbelaez, Diego G. [Posgrado en Ciencia e Ingenieria en Materiales, Instituto de Investigaciones en Materiales, Universidad Nacional Autonoma de Mexico, Av. Universidad 3000, C.P. 04510, Coyoacan, Mexico D.F. (Mexico); Departamento de Nanotecnologia, Centro de Fisica Aplicada y Tecnologia Avanzada, Universidad Nacional Autonoma de Mexico, Campus Juriquilla, Boulevard Juriquilla 3001, C.P. 76230, A.P. 1-1010, Juriquilla, Qro. (Mexico); Giraldo-Betancur, Astrid L. [Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional, Libramiento Norponiente 2000, C.P. 76230, Fracc. Real de Juriquilla, Qro. (Mexico); Hernandez-Urbiola, Margarita I. [Posgrado en Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Campus Juriquilla, Boulevard Juriquilla 3001, C.P. 76230, A.P. 1-1010, Juriquilla, Qro. (Mexico); Departamento de Nanotecnologia, Centro de Fisica Aplicada y Tecnologia Avanzada, Universidad Nacional Autonoma de Mexico, Campus Juriquilla, Boulevard Juriquilla 3001, C.P. 76230, A.P. 1-1010, Juriquilla, Qro. (Mexico); Rodriguez-Garcia, Mario E. [Departamento de Nanotecnologia, Centro de Fisica Aplicada y Tecnologia Avanzada, Universidad Nacional Autonoma de Mexico, Campus Juriquilla, Boulevard Juriquilla 3001, C.P. 76230, A.P. 1-1010, Juriquilla, Qro. (Mexico)

    2011-12-15

    Bones are the support of the body. They are composed of many inorganic compounds and other organic materials that all together can be used to determine the mineral density of the bones. The bone mineral density is a measure index that is widely used as an indicator of the health of the bone. A typical manner to evaluate the quality of the bone is a densitometry study; a dual x-ray absorptiometry system based study that has been widely used to assess the mineral density of some animals' bones. However, despite the success stories of utilizing these systems in many different applications, it is a very expensive method that requires frequent calibration processes to work properly. Moreover, its usage in small species applications (e.g., rodents) has not been quite demonstrated yet. Following this argument, it is suggested that there is a need for an instrument that would perform such a task in a more reliable and economical manner. Therefore, in this paper we explore the possibility to develop a new, affordable, and reliable single x-ray absorptiometry system. The method consists of utilizing a single x-ray source, an x-ray image sensor, and a computer platform that all together, as a whole, will allow us to calculate the mineral density of the bone. Utilizing an x-ray transmission theory modified through a version of the Lambert-Beer law equation, a law that expresses the relationship among the energy absorbed, the thickness, and the absorption coefficient of the sample at the x-rays wavelength to calculate the mineral density of the bone can be advantageous. Having determined the parameter equation that defines the ratio of the pixels in radiographies and the bone mineral density [measured in mass per unit of area (g/cm{sup 2})], we demonstrated the utility of our novel methodology by calculating the mineral density of Wistar rats' femur bones.

  10. Spectrophotometric high-precision seawater pH determination for use in underway measuring systems

    Directory of Open Access Journals (Sweden)

    S. Aßmann

    2011-06-01

    Full Text Available Autonomous sensors are required for a comprehensive documentation of the changes in the marine carbon system and thus to differentiate between its natural variability and anthropogenic impacts. Spectrophotometric determination of pH – a key variable of the seawater carbon system – is particularly suited to achieve precise and drift-free measurements. However, available spectrophotometric instruments are not suitable for integration into automated measurement systems (e.g. FerryBox since they do not meet the major requirements of reliability, stability, robustness and moderate cost. Here we report on the development and testing of a new indicator-based pH sensor that meets all of these requirements. This sensor can withstand the rough conditions during long-term deployments on ships of opportunities and is applicable on the open ocean as well as in coastal waters with complex background and highly variable conditions. The sensor uses a high resolution CCD spectrometer as detector connected via optical fibers to a custom-made cuvette designed to reduce the impact of air bubbles. The sample temperature can be precisely adjusted (25 °C ± 0.006 °C using computer-controlled power supplies and Peltier elements thus avoiding the widely used water bath. The overall setup achieves a measurement frequency of 1 min−1 with a precision of ± 0.0007 pH units and an average offset of +0.0018 pH units to a pH reference during shipboard operation. Application of this sensor allows monitoring of seawater pH in autonomous underway systems, providing a key variable for characterization and understanding the marine carbon system.

  11. Determinants of Pseudomonas putida WCS358 involved in inducing systemic resistance in plants.

    Science.gov (United States)

    Meziane, Hamid; VAN DER Sluis, Ientse; VAN Loon, Leendert C; Höfte, Monica; Bakker, Peter A H M

    2005-03-01

    SUMMARY Pseudomonas putida WCS358 is a plant growth-promoting rhizobacterium originally isolated from the rhizosphere of potato. It can suppress soil-borne plant diseases by siderophore-mediated competition for iron, but it has also been reported to result in induced systemic resistance (ISR) in Arabidopsis thaliana. Bacterial determinants of this strain involved in inducing systemic resistance in Arabidopsis were investigated using a Tn5 transposon mutant defective in biosynthesis of the fluorescent siderophore pseudobactin, a non-motile Tn5 mutant lacking flagella, and a spontaneous phage-resistant mutant lacking the O-antigenic side chain of the lipopolysaccharides (LPS). When using Pseudomonas syringae pv. tomato as the challenging pathogen, purified pseudobactin, flagella and LPS all triggered ISR. However, the mutants were all as effective as the parental strain, suggesting redundancy in ISR-triggering traits in WCS358. The Botrytis cinerea-tomato, B. cinerea-bean and Colletotrichum lindemuthianum-bean model systems were used to test further the potential of P. putida WCS358 to induce ISR. Strain WCS358 significantly reduced disease development in all three systems, indicating that also on tomato and bean WCS358 can trigger ISR. In both tomato and bean, the LPS mutant had lost the ability to induce resistance, whereas the flagella mutant was still effective. In bean, the pseudobactin mutant was still effective, whereas this mutant has lost its effectivity in tomato. In both bean and tomato, flagella isolated from the parental strain were not effective, whereas LPS or pseudobactin did induce systemic resistance.

  12. Simple flow injection colorimetric system for determination of paraquat in natural water.

    Science.gov (United States)

    Chuntib, Prakit; Jakmunee, Jaroon

    2015-11-01

    A simple and low cost flow injection colorimetric system has been developed for determination of paraquat in natural water. The developed method is based on the reduction of paraquat by using sodium dithionite as a reducing agent in an alkaline medium to produce a blue free radical ion that can be detected by a simple light emitting diode-light dependent resistor (LED-LDR) colorimeter. The standard or sample solution was injected via a set of 3-way solenoid valves into a water carrier stream and flowed to merge with reagent to generate a colored product which is proportional to the concentration of paraquat ion in the solution. Under the optimum condition of the system, i.e., mixing coil length 30 cm, flow rate 2.0 mL min(-1), sample volume 100 μL, concentrations of dithionite 0.1% (w/v) and sodium hydroxide 0.06 mol L(-1), a linear calibration graph in the range of 0.2-10.0 mg L(-1) with a correlation coefficient of 0.9996, and a limit of detection of 0.15 mg L(-1) were achieved. Relative standard deviation for 9 replicate injections of 1 mg L(-1) paraquat is 3.7%. A sample throughput of 40 injections h(-1) was achieved. The limit of detection can be improved by off-line preconcentration of paraquat employing a column packed with Dowex 50WX8-100 (H) cation exchange resin and eluted with 10% (w/v) ammonium chloride in ammonium buffer solution pH 10. The eluting solution was then injected into the FI system for paraquat determination. The proposed system did not suffer from interferences of some possible ions in natural water and other herbicides. Recoveries obtained by spiking 0.5 and 5.0 mg L(-1) paraquat standard into water samples were in the range of 104-110% and 101-105%, respectively. The developed system can be conveniently applied for screening of paraquat contaminated in natural water.

  13. Cross-reactivity of TDX and OPUS immunoassay systems for serum digoxin determination.

    Science.gov (United States)

    Okazaki, M; Tanigawara, Y; Kita, T; Komada, F; Okumura, K

    1997-12-01

    The properties of the widely used TDX Analyzer and recently developed OPUS Immunoassay System were compared using 403 serum specimens taken from patients who did or did not take digoxin. Of the 210 specimens from patients not treated with digoxin, a false- positive digoxin concentration was detected in 15 specimens (7%) by TDX and in only 2 specimens (1%) by OPUS because of the cross-reactivity with structurally similar drugs. Potassium canrenoate, digitoxin, deslanoside, and methyldigoxin exhibited marked concentration-dependent cross-reactivity in the TDX assay method, whereas deslanoside and methyldigoxin only showed cross-reactivity with the antibody used in the OPUS method. Although a poor correlation was observed between these two methods for the determination of 193 samples from patients treated with digoxin, the correlation was remarkably improved (r = 0.914) and the slope approximated unity when excluded the data from patients who were treated concurrently with the cross-reactive compounds. In routine TDM of digoxin, the authors experienced two cases in which cross-reactivity of the assay system caused a clinical problem. Concurrent administration of intravenous canrenoate apparently interfered with the digoxin assay by TDX, but this problem was solved by using the OPUS system. The authors found OPUS more useful for monitoring serum digoxin concentrations in patients because of its superior specificity.

  14. Absolute densities, masses, and radii of the WASP-47 system determined dynamically

    CERN Document Server

    Almenara, J M; Bonfils, X; Udry, S

    2016-01-01

    We present a self-consistent modelling of the available light curve and radial velocity data of WASP-47 that takes into account the gravitational interactions between all known bodies in the system. The joint analysis of light curve and radial velocity data in a multi-planetary system allows deriving absolute densities, radii, and masses without the use of theoretical stellar models. For WASP-47 the precision is limited by the reduced dynamical information that is due to the short time span of the K2 light curve. We achieve a precision of around 22% for the radii of the star and the transiting planets, between 40% and 60% for their masses, and between 1.5% and 38% for their densities. All values agree with previously reported measurements. When theoretical stellar models are included, the system parameters are determined with a precision that exceeds that achieved by previous studies, thanks to the self-consistent modelling of light curve and radial velocity data.

  15. Optical techniques for determination of the state of cure of epoxy resin based systems

    Science.gov (United States)

    Michie, W. C.; Thursby, G.; Johnstone, W.; Culshaw, B.

    1993-03-01

    Determination of the state of cure of epoxy resin based systems is of considerable interest to manufacturers of large carbon fiber reinforced plastic and glass reinforced plastic structures. Optical methods designed to indicate the cure state have been developed using a loss mechanism which is a function of the refractive index of the curing system. Such techniques are however subject to corruption from losses arising from other influences and consequently are limited in their measurement resolution. In this paper, two techniques which are able to provide a high degree of accuracy of measurement of refractive index are investigated as a means of performing cure measurements. The methods investigated involve the interaction of the evanescent field of a side polished optical fiber with an overlay waveguide or a surface plasmon. Coupling between the fiber and the overlay waveguide (or plasmon) is strongly influenced by the refractive index of the bulk superstrate above the overlay (in this case the curing resin system). Both sensing schemes are self referencing and are not influenced by loss.

  16. Absolute densities, masses, and radii of the WASP-47 system determined dynamically

    Science.gov (United States)

    Almenara, J. M.; Díaz, R. F.; Bonfils, X.; Udry, S.

    2016-10-01

    We present a self-consistent modelling of the available light curve and radial velocity data of WASP-47 that takes into account the gravitational interactions between all known bodies in the system. The joint analysis of light curve and radial velocity data in a multi-planetary system allows deriving absolute densities, radii, and masses without the use of theoretical stellar models. For WASP-47 the precision is limited by the reduced dynamical information that is due to the short time span of the K2 light curve. We achieve a precision of around 22% for the radii of the star and the transiting planets, between 40% and 60% for their masses, and between 1.5% and 38% for their densities. All values agree with previously reported measurements. When theoretical stellar models are included, the system parameters are determined with a precision that exceeds that achieved by previous studies, thanks to the self-consistent modelling of light curve and radial velocity data.

  17. A miniature shoe-mounted orientation determination system for accurate indoor heading and trajectory tracking

    Science.gov (United States)

    Zhang, Shengzhi; Yu, Shuai; Liu, Chaojun; Liu, Sheng

    2016-06-01

    Tracking the position of pedestrian is urgently demanded when the most commonly used GPS (Global Position System) is unavailable. Benefited from the small size, low-power consumption, and relatively high reliability, micro-electro-mechanical system sensors are well suited for GPS-denied indoor pedestrian heading estimation. In this paper, a real-time miniature orientation determination system (MODS) was developed for indoor heading and trajectory tracking based on a novel dual-linear Kalman filter. The proposed filter precludes the impact of geomagnetic distortions on pitch and roll that the heading is subjected to. A robust calibration approach was designed to improve the accuracy of sensors measurements based on a unified sensor model. Online tests were performed on the MODS with an improved turntable. The results demonstrate that the average RMSE (root-mean-square error) of heading estimation is less than 1°. Indoor heading experiments were carried out with the MODS mounted on the shoe of pedestrian. Besides, we integrated the existing MODS into an indoor pedestrian dead reckoning application as an example of its utility in realistic actions. A human attitude-based walking model was developed to calculate the walking distance. Test results indicate that mean percentage error of indoor trajectory tracking achieves 2% of the total walking distance. This paper provides a feasible alternative for accurate indoor heading and trajectory tracking.

  18. Determining the optimal number of Kanban in multi-products supply chain system

    Science.gov (United States)

    Widyadana, G. A.; Wee, H. M.; Chang, Jer-Yuan

    2010-02-01

    Kanban, a key element of just-in-time system, is a re-order card or signboard giving instruction or triggering the pull system to manufacture or supply a component based on actual usage of material. There are two types of Kanban: production Kanban and withdrawal Kanban. This study uses optimal and meta-heuristic methods to determine the Kanban quantity and withdrawal lot sizes in a supply chain system. Although the mix integer programming method gives an optimal solution, it is not time efficient. For this reason, the meta-heuristic methods are suggested. In this study, a genetic algorithm (GA) and a hybrid of genetic algorithm and simulated annealing (GASA) are used. The study compares the performance of GA and GASA with that of the optimal method using MIP. The given problems show that both GA and GASA result in a near optimal solution, and they outdo the optimal method in term of run time. In addition, the GASA heuristic method gives a better performance than the GA heuristic method.

  19. An in situ filtration system for trace element determination in suspended particulate matter

    Energy Technology Data Exchange (ETDEWEB)

    Grotti, Marco; Soggia, Francesco; Dalla Riva, Simona; Magi, Emanuele; Frache, Roberto

    2003-11-28

    A system for in situ filtration of suspended particulate matter (SPM) has been developed specifically for trace element determination. Minimization of metal contamination sources was realized by careful choice of materials and designing a ''closed-open-closed'' electronic procedure for the soaking of the system. In order to prevent undesired pressure increase due to the filter clogging and to avoid modification of metal distribution in the different phases of SPM, a relief valve was used to keep the pumping pressure constant. The possibility to perform a sub-sampling of SPM was also taken into account to expand the analytical capabilities. Finally, the sampler was equipped with a multiparametric probe in order to carry out real-time measurements of physical parameters (temperature, salinity, fluorescence, turbidimetry) and operating conditions (flow rates, filtered volumes, energy consumption). The system has been tested and applied successfully in Antarctic coastal waters (Terra Nova Bay, Ross Sea) in the framework of the Italian Research Programme in Antarctica (PNRA). The analytical possibilities allowed by the large amount of SPM which can be collected by FIS500 (50-100 mg) include total metal concentration, solid speciation and morphological investigation by scanning electron microscopy.

  20. Method of determining effects of heat-induced irregular refractive index on an optical system.

    Science.gov (United States)

    Song, Xifa; Li, Lin; Huang, Yifan

    2015-09-01

    The effects of an irregular refractive index on optical performance are examined. A method was developed to express a lens's irregular refractive index distribution. An optical system and its mountings were modeled by a thermomechanical finite element (FE) program in the predicted operating temperature range, -45°C-50°C. FE outputs were elaborated using a MATLAB optimization routine; a nonlinear least squares algorithm was adopted to determine which gradient equation best fit each lens's refractive index distribution. The obtained gradient data were imported into Zemax for sequential ray-tracing analysis. The root mean square spot diameter, modulation transfer function, and diffraction ensquared energy were computed for an optical system under an irregular refractive index and under thermoelastic deformation. These properties are greatly reduced by the irregular refractive index effect, which is one-third to five-sevenths the size of the thermoelastic deformation effect. Thus, thermal analyses of optical systems should consider not only thermoelastic deformation but also refractive index irregularities caused by inhomogeneous temperature.