WorldWideScience

Sample records for biomolecular systems determinants

  1. Biomolecular Structure Determination with Divide and Concur

    Science.gov (United States)

    Kallus, Yoav; Elser, Veit

    2009-03-01

    Divide and concur (D-C) is a general computational approach, designed for the solution of highly frustrated problems. Recently applied to the problems of disk packing, the kissing number problem, and 3-SAT, it was competitive or outperformed special-purpose methods.ootnotetextS. Gravel and V. Elser, Phys. Rev. E 78, 036706 (2008) We present a method for applying the D-C framework to the problem of biomolecular structure determination. From a list of geometric constraints on groups of atoms in the molecule, we construct a deterministic iterative map that efficiently searches for structures simultaneously satisfying all constraints. As our method eschews an energy function and its minimization to focus on geometric constraints, it can very naturally integrate with the geometric constraints due to chemistry and physics, experimental constraints due to NMR data or many other experimental or biological hints. We present some results of our method.

  2. 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.

  3. 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.

  4. 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.

  5. A multiscale modeling approach for biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Bowling, Alan, E-mail: bowling@uta.edu; Haghshenas-Jaryani, Mahdi, E-mail: mahdi.haghshenasjaryani@mavs.uta.edu [The University of Texas at Arlington, Department of Mechanical and Aerospace Engineering (United States)

    2015-04-15

    This paper presents a new multiscale molecular dynamic model for investigating the effects of external interactions, such as contact and impact, during stepping and docking of motor proteins and other biomolecular systems. The model retains the mass properties ensuring that the result satisfies Newton’s second law. This idea is presented using a simple particle model to facilitate discussion of the rigid body model; however, the particle model does provide insights into particle dynamics at the nanoscale. The resulting three-dimensional model predicts a significant decrease in the effect of the random forces associated with Brownian motion. This conclusion runs contrary to the widely accepted notion that the motor protein’s movements are primarily the result of thermal effects. This work focuses on the mechanical aspects of protein locomotion; the effect ATP hydrolysis is estimated as internal forces acting on the mechanical model. In addition, the proposed model can be numerically integrated in a reasonable amount of time. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of myosin V.

  6. 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

  7. Quantifying Modularity in the Evolution of Biomolecular Systems

    OpenAIRE

    2004-01-01

    Functional modules are considered the primary building blocks of biomolecular systems. Here we study to what extent functional modules behave cohesively across genomes:That is, are functional modules also evolutionary modules? We probe this question by analyzing for a large collection of functional modules the phyletic patterns of their genes across 110 genomes. The majority of functional modules display limited evolutionary modularity. This result confirms certain comparative genome analyses...

  8. Role of biomolecular logic systems in biosensors and bioactuators

    Science.gov (United States)

    Mailloux, Shay; Katz, Evgeny

    2014-09-01

    An overview of recent advances in biosensors and bioactuators based on biocomputing systems is presented. Biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce an output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, the biocomputing approach enables high-fidelity multianalyte biosensing, which is particularly beneficial for biomedical applications. Multisignal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert medical personnel of medical emergencies together with immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly as exemplified for liver injury. Wide-ranging applications of multianalyte digital biosensors in medicine, environmental monitoring, and homeland security are anticipated. "Smart" bioactuators, for signal-triggered drug release, for example, were designed by interfacing switchable electrodes with biocomputing systems. Integration of biosensing and bioactuating systems with biomolecular information processing systems advances the potential for further scientific innovations and various practical applications.

  9. Biomolecular logic systems: applications to biosensors and bioactuators

    Science.gov (United States)

    Katz, Evgeny

    2014-05-01

    The paper presents an overview of recent advances in biosensors and bioactuators based on the biocomputing concept. Novel biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multi-analyte biosensing, particularly beneficial for biomedical applications. Multi-signal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert to medical emergencies, along with an immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly exemplified for liver injury. Wide-ranging applications of multi-analyte digital biosensors in medicine, environmental monitoring and homeland security are anticipated. "Smart" bioactuators, for example for signal-triggered drug release, were designed by interfacing switchable electrodes and biocomputing systems. Integration of novel biosensing and bioactuating systems with the biomolecular information processing systems keeps promise for further scientific advances and numerous practical applications.

  10. Perspective: Coarse-grained models for biomolecular systems

    Science.gov (United States)

    Noid, W. G.

    2013-09-01

    By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.

  11. PREFACE: Radiation Damage in Biomolecular Systems (RADAM07)

    Science.gov (United States)

    McGuigan, Kevin G.

    2008-03-01

    The annual meeting of the COST P9 Action `Radiation damage in biomolecular systems' took place from 19-22 June 2007 in the Royal College of Surgeons in Ireland, in Dublin. The conference was structured into 5 Working Group sessions: Electrons and biomolecular interactions Ions and biomolecular interactions Radiation in physiological environments Theoretical developments for radiation damage Track structure in cells Each of the five working groups presented two sessions of invited talks. Professor Ron Chesser of Texas Tech University, USA gave a riveting plenary talk on `Mechanisms of Adaptive Radiation Responses in Mammals at Chernobyl' and the implications his work has on the Linear-No Threshold model of radiation damage. In addition, this was the first RADAM meeting to take place after the Alexander Litvenenko affair and we were fortunate to have one of the leading scientists involved in the European response Professor Herwig Paretzke of GSF-Institut für Strahlenschutz, Neuherberg, Germany, available to speak. The remaining contributions were presented in the poster session. A total of 72 scientific contributions (32 oral, 40 poster), presented by 97 participants from 22 different countries, gave an overview on the current progress in the 5 different subfields. A 1-day pre-conference `Early Researcher Tutorial Workshop' on the same topic kicked off on 19 June attended by more than 40 postgrads, postdocs and senior researchers. Twenty papers, based on these reports, are included in this volume of Journal of Physics: Conference Series. All the contributions in this volume were fully refereed, and they represent a sample of the courses, invited talks and contributed talks presented during RADAM07. The interdisciplinary RADAM07 conference brought together researchers from a variety of different fields with a common interest in biomolecular radiation damage. This is reflected by the disparate backgrounds of the authors of the papers presented in these proceedings

  12. Effect of antibody modifications on its biomolecular binding as determined by surface plasmon resonance.

    Science.gov (United States)

    Vashist, Sandeep Kumar

    2012-02-01

    A surface plasmon resonance (SPR)-based procedure was developed to determine the effect of antibody modifications on its biomolecular binding behavior. Mouse immunoglobulin G (IgG) was immobilized on a protein A-functionalized gold-coated SPR chip. Goat anti-mouse IgG and its various commercially available modifications (i.e., conjugated with atto 550, atto 647, tetramethylrhodamine isothiocyanate [TRITC], horseradish peroxidase [HRP], or biotin) were employed in exactly the same concentration for the detection of mouse IgG. The various modifications of goat anti-mouse IgG decreased its biomolecular binding to mouse IgG in the order of unmodified>HRP-labeled>atto 550-labeled>biotinylated>TRITC-labeled>atto 647-labeled. PMID:22093612

  13. 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

  14. Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES

    OpenAIRE

    Chennubhotla, Chakra; Bahar, Ivet

    2006-01-01

    We introduce a novel approach for elucidating the potential pathways of allosteric communication in biomolecular systems. The methodology, based on Markov propagation of ‘information' across the structure, permits us to partition the network of interactions into soft clusters distinguished by their coherent stochastics. Probabilistic participation of residues in these clusters defines the communication patterns inherent to the network architecture. Application to bacterial chaperonin complex ...

  15. Biomolecular Science (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-04-01

    A brief fact sheet about NREL Photobiology and Biomolecular Science. The research goal of NREL's Biomolecular Science is to enable cost-competitive advanced lignocellulosic biofuels production by understanding the science critical for overcoming biomass recalcitrance and developing new product and product intermediate pathways. NREL's Photobiology focuses on understanding the capture of solar energy in photosynthetic systems and its use in converting carbon dioxide and water directly into hydrogen and advanced biofuels.

  16. 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 de...

  17. Active learning for discovery in the laboratory: characterising biomolecular systems

    OpenAIRE

    Lovell, Chris

    2012-01-01

    Resource costs are a limiting factor in many real-world problems. For example, a chemist or biologist may only be able to afford a limited number of chemicals that can be used to perform experiments that examine a hypothesis. A domain expert may only have a limited amount time they can spend analysing a dataset. An inaccessible remote sensor or robotic exploratory system may only have a limited communications bandwidth through which data can be transmitted. In each case there is a strong requ...

  18. An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support

    Energy Technology Data Exchange (ETDEWEB)

    Fei, Yiyan; Landry, James P.; Zhu, X. D., E-mail: xdzhu@physics.ucdavis.edu [Department of Physics, University of California, One Shields Avenue, Davis, California 95616 (United States); Li, Yanhong; Yu, Hai; Lau, Kam; Huang, Shengshu; Chokhawala, Harshal A.; Chen, Xi [Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616 (United States)

    2013-11-15

    A biological state is equilibrium of multiple concurrent biomolecular reactions. The relative importance of these reactions depends on physiological temperature typically between 10 °C and 50 °C. Experimentally the temperature dependence of binding reaction constants reveals thermodynamics and thus details of these biomolecular processes. We developed a variable-temperature opto-fluidic system for real-time measurement of multiple (400–10 000) biomolecular binding reactions on solid supports from 10 °C to 60 °C within ±0.1 °C. We illustrate the performance of this system with investigation of binding reactions of plant lectins (carbohydrate-binding proteins) with 24 synthetic glycans (i.e., carbohydrates). We found that the lectin-glycan reactions in general can be enthalpy-driven, entropy-driven, or both, and water molecules play critical roles in the thermodynamics of these reactions.

  19. Calculating free-energy profiles in biomolecular systems from fast nonequilibrium processes

    Science.gov (United States)

    Forney, Michael W.; Janosi, Lorant; Kosztin, Ioan

    2008-11-01

    Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin , J. Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by different methods. Our approach appears to be about one order of magnitude faster than the other PMF calculation methods and, in addition, it also provides the position-dependent diffusion coefficient along the RC. Thus, the obtained PMF and diffusion coefficient can be used in an overdamped Brownian model to estimate important characteristics of the studied systems, e.g., the mean folding time of the stretched deca-alanine and the mean diffusion time of the potassium ion through gramicidin A.

  20. Calculating free energy profiles in biomolecular systems from fast non-equilibrium processes

    CERN Document Server

    Forney, Michael; Kosztin, Ioan

    2008-01-01

    Often gaining insight into the functioning of biomolecular systems requires to follow their dynamics along a microscopic reaction coordinate (RC) on a macroscopic time scale, which is beyond the reach of current all atom molecular dynamics (MD) simulations. A practical approach to this inherently multiscale problem is to model the system as a fictitious overdamped Brownian particle that diffuses along the RC in the presence of an effective potential of mean force (PMF) due to the rest of the system. By employing the recently proposed FR method [I. Kosztin et al., J. of Chem. Phys. 124, 064106 (2006)], which requires only a small number of fast nonequilibrium MD simulations of the system in both forward and time reversed directions along the RC, we reconstruct the PMF: (1) of deca-alanine as a function of its end-to-end distance, and (2) that guides the motion of potassium ions through the gramicidin A channel. In both cases the computed PMFs are found to be in good agreement with previous results obtained by ...

  1. 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.

  2. Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.

    Directory of Open Access Journals (Sweden)

    Alexander V Ratushny

    2011-06-01

    Full Text Available When living systems detect changes in their external environment their response must be measured to balance the need to react appropriately with the need to remain stable, ignoring insignificant signals. Because this is a fundamental challenge of all biological systems that execute programs in response to stimuli, we developed a generalized time-frequency analysis (TFA framework to systematically explore the dynamical properties of biomolecular networks. Using TFA, we focused on two well-characterized yeast gene regulatory networks responsive to carbon-source shifts and a mammalian innate immune regulatory network responsive to lipopolysaccharides (LPS. The networks are comprised of two different basic architectures. Dual positive and negative feedback loops make up the yeast galactose network; whereas overlapping positive and negative feed-forward loops are common to the yeast fatty-acid response network and the LPS-induced network of macrophages. TFA revealed remarkably distinct network behaviors in terms of trade-offs in responsiveness and noise suppression that are appropriately tuned to each biological response. The wild type galactose network was found to be highly responsive while the oleate network has greater noise suppression ability. The LPS network appeared more balanced, exhibiting less bias toward noise suppression or responsiveness. Exploration of the network parameter space exposed dramatic differences in system behaviors for each network. These studies highlight fundamental structural and dynamical principles that underlie each network, reveal constrained parameters of positive and negative feedback and feed-forward strengths that tune the networks appropriately for their respective biological roles, and demonstrate the general utility of the TFA approach for systems and synthetic biology.

  3. Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density

    International Nuclear Information System (INIS)

    Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein-protein complexes.

  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. 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

    2016-01-01

    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. PMID:27399702

  6. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    International Nuclear Information System (INIS)

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks

  7. 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...

  8. Studies of the charge instabilities in the complex nano-objects: clusters and bio-molecular systems

    International Nuclear Information System (INIS)

    For the last 6 years, my main research works focused on i) the Coulomb instabilities and the fragmentation processes of fullerenes and clusters of fullerenes ii) the stability and the reactivity of complex bio-molecular systems. Concerning the clusters of fullerenes, which are van der Waals type clusters, we have shown that the multiply charged species, obtained in collisions with slow highly charged ions, keep their structural properties but become very good electric conductor. In another hand, with the aim to understand the role of the biologic environment at the molecular scale in the irradiation damage of complex biomolecules, we have studied the charge stabilities of clusters of small biomolecules and the dissociation processes of larger nano-hydrated biomolecules. Theses studies have shown that first, specific molecular recognition mechanisms continue to exist in gas phase and secondly, a small and very simple biochemical environment is enough to change the dynamics of instabilities. (author)

  9. 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. PMID:26989950

  10. 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; Lin, Guang; Baker, Nathan A.

    2015-12-31

    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.

  11. 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

  12. Bi-stability of amplitude modulation AFM in air: deterministic and stochastic outcomes for imaging biomolecular systems

    International Nuclear Information System (INIS)

    The dynamics of the oscillating microcantilever for amplitude modulation atomic force microscopy (AM AFM) operating in air is well understood theoretically but the experimental outcomes are still emerging. We use double-stranded DNA on mica as a model biomolecular system for investigating the connection between theory and experiment. A demonstration that the switching between the two cantilever oscillation states is stochastic in nature is achieved, and it can be induced by means of topographical anomalies on the surface. Whether one or the other attractor basin is accessed depends on the tip-sample separation history used to achieve the imaging conditions, and we show that the behaviour is reproducible when the tip is stable and well characterized. Emergence of background noise occurs in certain regions of parameter space regardless of whether two cantilever oscillation states coexist. The low state has been explored in detail and we note that at low to intermediate values of the free amplitude, noise-free imaging is achieved. The outcomes shown here are general and demonstrate that a thorough and systematic experimental approach in conjunction with standard modelling gives insight into the mechanisms behind image contrast formation in AM AFM in air.

  13. Model for the fast estimation of basis set superposition error in biomolecular systems

    Science.gov (United States)

    Faver, John C.; Zheng, Zheng; Merz, Kenneth M.

    2011-01-01

    Basis set superposition error (BSSE) is a significant contributor to errors in quantum-based energy functions, especially for large chemical systems with many molecular contacts such as folded proteins and protein-ligand complexes. While the counterpoise method has become a standard procedure for correcting intermolecular BSSE, most current approaches to correcting intramolecular BSSE are simply fragment-based analogues of the counterpoise method which require many (two times the number of fragments) additional quantum calculations in their application. We propose that magnitudes of both forms of BSSE can be quickly estimated by dividing a system into interacting fragments, estimating each fragment's contribution to the overall BSSE with a simple statistical model, and then propagating these errors throughout the entire system. Such a method requires no additional quantum calculations, but rather only an analysis of the system's interacting fragments. The method is described herein and is applied to a protein-ligand system, a small helical protein, and a set of native and decoy protein folds. PMID:22010701

  14. Ion interaction with biomolecular systems and the effect of the environment

    Science.gov (United States)

    Domaracka, Alicja; Capron, Michael; Maclot, Sylvain; Chesnel, Jean-Yves; Méry, Alain; Poully, Jean-Christophe; Rangama, Jimmy; Adoui, Lamri; Rousseau, Patrick; Huber, Bernd A.

    2012-07-01

    To fully understand the mechanisms of radiation damage in living tissues, a detailed knowledge of the processes occurring at the molecular level is needed. In the gas phase, most of the investigations concerning the ionization and fragmentation of biologically relevant molecular systems are performed with isolated molecules. The importance of such studies is limited to the intrinsic properties of these molecules because of the lack of a chemical environment. To probe the effect of such an environment on the behavior of small biomolecules under irradiation, the molecules (α-amino acids, adenine) were embedded into clusters. The present results, obtained with multiply charged ions, clearly indicate the protective role of the clusters since the total fragmentation yield is reduced for all systems. The surrounding molecules allow for a redistribution of the excess energy and of the charge within the cluster. In the case of adenine clusters, a new fragmentation channel is identified. Moreover, for hydrated adenine clusters, low-energy ion induced chemical reactions are observed, namely the proton transfer from the water cluster to the adenine molecule.

  15. Ion interaction with biomolecular systems and the effect of the environment

    International Nuclear Information System (INIS)

    To fully understand the mechanisms of radiation damage in living tissues, a detailed knowledge of the processes occurring at the molecular level is needed. In the gas phase, most of the investigations concerning the ionization and fragmentation of biologically relevant molecular systems are performed with isolated molecules. The importance of such studies is limited to the intrinsic properties of these molecules because of the lack of a chemical environment. To probe the effect of such an environment on the behavior of small biomolecules under irradiation, the molecules (α-amino acids, adenine) were embedded into clusters. The present results, obtained with multiply charged ions, clearly indicate the protective role of the clusters since the total fragmentation yield is reduced for all systems. The surrounding molecules allow for a redistribution of the excess energy and of the charge within the cluster. In the case of adenine clusters, a new fragmentation channel is identified. Moreover, for hydrated adenine clusters, low-energy ion induced chemical reactions are observed, namely the proton transfer from the water cluster to the adenine molecule.

  16. Programming in Biomolecular Computation:

    DEFF Research Database (Denmark)

    Hartmann, Lars; 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...... 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...

  17. Advances in integrative modeling of biomolecular complexes

    NARCIS (Netherlands)

    Karaca, E.; Bonvin, A.M.J.J.

    2013-01-01

    High-resolution structural information is needed in order to unveil the underlying mechanistic of biomolecular function. Due to the technical limitations or the nature of the underlying complexes, acquiring atomic resolution information is difficult for many challenging systems, while, often, low-re

  18. 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 ). PMID:27023095

  19. Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

    OpenAIRE

    Garg, Sahil; Galstyan, Aram; Hermjakob, Ulf; Marcu, Daniel

    2015-01-01

    We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sen...

  20. 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....

  1. Membrane-based biomolecular smart materials

    International Nuclear Information System (INIS)

    Membrane-based biomolecular materials are a new class of smart material that feature networks of artificial lipid bilayers contained within durable synthetic substrates. Bilayers contained within this modular material platform provide an environment that can be tailored to host an enormous diversity of functional biomolecules, where the functionality of the global material system depends on the type(s) and organization(s) of the biomolecules that are chosen. In this paper, we review a series of biomolecular material platforms developed recently within the Leo Group at Virginia Tech and we discuss several novel coupling mechanisms provided by these hybrid material systems. The platforms developed demonstrate that the functions of biomolecules and the properties of synthetic materials can be combined to operate in concert, and the examples provided demonstrate how the formation and properties of a lipid bilayer can respond to a variety of stimuli including mechanical forces and electric fields

  2. Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

    OpenAIRE

    2009-01-01

    Background Identification of functionally important sites in biomolecular sequences has broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks. Experimental determination of such sites lags far behind the number of known biomolecular sequences. Hence, there is a need to develop reliable computational methods for identifying functionally important sites from biomolecular sequences. Results We present a mixture of experts approach to b...

  3. Analyzing biomolecular interactions by variable angle ellipsometry

    Science.gov (United States)

    Wu, Jiun-Yan; Lee, Chih-Kung; Lee, J. H.; Shiue, Shuen-Chen; Lee, Shu-Sheng; Lin, Shiming

    2001-10-01

    In this paper, an innovative ellipsometer is developed and applied to metrology of the biomolecular interaction on a protein biochip. Both the theory, optical and opto-mechanical configurations of this newly developed ellipsometer and methodologies adopted in system design to improve the system performance are presented. It will be shown that by measuring the ellipsometric parameters, the corresponding concentration variation in biochemical reaction can be calculated according to stoichiometry analysis. By applying the variable angle ellipsometry to analysis of a multi-layered sample, the thickness and concentration are resolved. It is believed that the newly developed ellipsometer biosensor is able to undertake an accurate measurement on biomedical interaction.

  4. 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.

  5. 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.

  6. NMscatt: a program for calculating inelastic scattering from large biomolecular systems using classical force-field simulations

    CERN Document Server

    Merzel, F; Johnson, M R; Fontaine-Vive, Fabien; Johnson, Mark R.; Merzel, Franci

    2006-01-01

    Computational tools for normal mode analysis, which are widely used in physics and materials science problems, are designed here in a single package called NMscatt (Normal Modes & scattering) that allows arbitrarily large systems to be handled. The package allows inelastic neutron and X-ray scattering observables to be calculated, allowing comparison with experimental data produced at large scale facilities. Various simplification schemes are presented for analysing displacement vectors, which are otherwise too complicated to understand in very large systems.

  7. 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...

  8. 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

  9. Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics.

    Science.gov (United States)

    Wu, Xiongwu; Damjanovic, Ana; Brooks, Bernard R

    2012-01-31

    This review provides a comprehensive description of the self-guided Langevin dynamics (SGLD) and the self-guided molecular dynamics (SGMD) methods and their applications. Example systems are included to provide guidance on optimal application of these methods in simulation studies. SGMD/SGLD has enhanced ability to overcome energy barriers and accelerate rare events to affordable time scales. It has been demonstrated that with moderate parameters, SGLD can routinely cross energy barriers of 20 kT at a rate that molecular dynamics (MD) or Langevin dynamics (LD) crosses 10 kT barriers. The core of these methods is the use of local averages of forces and momenta in a direct manner that can preserve the canonical ensemble. The use of such local averages results in methods where low frequency motion "borrows" energy from high frequency degrees of freedom when a barrier is approached and then returns that excess energy after a barrier is crossed. This self-guiding effect also results in an accelerated diffusion to enhance conformational sampling efficiency. The resulting ensemble with SGLD deviates in a small way from the canonical ensemble, and that deviation can be corrected with either an on-the-fly or a post processing reweighting procedure that provides an excellent canonical ensemble for systems with a limited number of accelerated degrees of freedom. Since reweighting procedures are generally not size extensive, a newer method, SGLDfp, uses local averages of both momenta and forces to preserve the ensemble without reweighting. The SGLDfp approach is size extensive and can be used to accelerate low frequency motion in large systems, or in systems with explicit solvent where solvent diffusion is also to be enhanced. Since these methods are direct and straightforward, they can be used in conjunction with many other sampling methods or free energy methods by simply replacing the integration of degrees of freedom that are normally sampled by MD or LD. PMID:23913991

  10. ORAC: a molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level.

    Science.gov (United States)

    Marsili, Simone; Signorini, Giorgio Federico; Chelli, Riccardo; Marchi, Massimo; Procacci, Piero

    2010-04-15

    We present the new release of the ORAC engine (Procacci et al., Comput Chem 1997, 18, 1834), a FORTRAN suite to simulate complex biosystems at the atomistic level. The previous release of the ORAC code included multiple time steps integration, smooth particle mesh Ewald method, constant pressure and constant temperature simulations. The present release has been supplemented with the most advanced techniques for enhanced sampling in atomistic systems including replica exchange with solute tempering, metadynamics and steered molecular dynamics. All these computational technologies have been implemented for parallel architectures using the standard MPI communication protocol. ORAC is an open-source program distributed free of charge under the GNU general public license (GPL) at http://www.chim.unifi.it/orac. PMID:19824035

  11. Storing and analysing biomolecular contacts

    OpenAIRE

    Walter, Peter

    2011-01-01

    Biomolecular contacts play a crucial role in all areas of life. In particular, protein-protein (PP) interactions are essential for most processes in biological cells. Antigen-antibody recognition, enzyme substrate binding, hormone receptor binding, RNA splicing, DNA replication and signal transduction are just some examples for the rich variety of PP interactions. In the last years modern proteomic methods have helped to get a better understanding of the complexity within living cell and orga...

  12. Models for solvated biomolecular structures

    OpenAIRE

    Cerutti, David

    2007-01-01

    Methods for estimating the structure and energetics of water around biomolecules are presented with the objective of improving the treatment of the biomolecular simulation environment as well as facilitating the use of complex, rigorous water models in the context of structure prediction problems that demand cheap solutions. Salt solutions around biomolecules are studied using an implicit solvent model with explicitly represented ions, revealing that the structure of the ion atmosphere is muc...

  13. 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

  14. 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...

  15. Abstractions for biomolecular computations

    CERN Document Server

    Okunoye, Babatunde O

    2008-01-01

    Deoxyribonucleic acid is increasingly being understood to be an informational molecule, capable of information processing.It has found application in the determination of non-deterministic algorithms and in the design of molecular computing devices. This is a theoretical analysis of the mathematical properties and relations of the molecules which constituting DNA, which explains in part why DNA is a successful computing molecule.

  16. Biomolecular detection employing the Interferometric Reflectance Imaging Sensor (IRIS).

    Science.gov (United States)

    Lopez, Carlos A; Daaboul, George G; Ahn, Sunmin; Reddington, Alexander P; Monroe, Margo R; Zhang, Xirui; Irani, Rostem J; Yu, Chunxiao; Genco, Caroline A; Cretich, Marina; Chiari, Marcella; Goldberg, Bennett B; Connor, John H; Ünlü, M Selim

    2011-01-01

    The sensitive measurement of biomolecular interactions has use in many fields and industries such as basic biology and microbiology, environmental/agricultural/biodefense monitoring, nanobiotechnology, and more. For diagnostic applications, monitoring (detecting) the presence, absence, or abnormal expression of targeted proteomic or genomic biomarkers found in patient samples can be used to determine treatment approaches or therapy efficacy. In the research arena, information on molecular affinities and specificities are useful for fully characterizing the systems under investigation. Many of the current systems employed to determine molecular concentrations or affinities rely on the use of labels. Examples of these systems include immunoassays such as the enzyme-linked immunosorbent assay (ELISA), polymerase chain reaction (PCR) techniques, gel electrophoresis assays, and mass spectrometry (MS). Generally, these labels are fluorescent, radiological, or colorimetric in nature and are directly or indirectly attached to the molecular target of interest. Though the use of labels is widely accepted and has some benefits, there are drawbacks which are stimulating the development of new label-free methods for measuring these interactions. These drawbacks include practical facets such as increased assay cost, reagent lifespan and usability, storage and safety concerns, wasted time and effort in labelling, and variability among the different reagents due to the labelling processes or labels themselves. On a scientific research basis, the use of these labels can also introduce difficulties such as concerns with effects on protein functionality/structure due to the presence of the attached labels and the inability to directly measure the interactions in real time. Presented here is the use of a new label-free optical biosensor that is amenable to microarray studies, termed the Interferometric Reflectance Imaging Sensor (IRIS), for detecting proteins, DNA, antigenic material

  17. A self-regulating biomolecular comparator for processing oscillatory signals.

    Science.gov (United States)

    Agrawal, Deepak K; Franco, Elisa; Schulman, Rebecca

    2015-10-01

    While many cellular processes are driven by biomolecular oscillators, precise control of a downstream on/off process by a biochemical oscillator signal can be difficult: over an oscillator's period, its output signal varies continuously between its amplitude limits and spends a significant fraction of the time at intermediate values between these limits. Further, the oscillator's output is often noisy, with particularly large variations in the amplitude. In electronic systems, an oscillating signal is generally processed by a downstream device such as a comparator that converts a potentially noisy oscillatory input into a square wave output that is predominantly in one of two well-defined on and off states. The comparator's output then controls downstream processes. We describe a method for constructing a synthetic biochemical device that likewise produces a square-wave-type biomolecular output for a variety of oscillatory inputs. The method relies on a separation of time scales between the slow rate of production of an oscillatory signal molecule and the fast rates of intermolecular binding and conformational changes. We show how to control the characteristics of the output by varying the concentrations of the species and the reaction rates. We then use this control to show how our approach could be applied to process different in vitro and in vivo biomolecular oscillators, including the p53-Mdm2 transcriptional oscillator and two types of in vitro transcriptional oscillators. These results demonstrate how modular biomolecular circuits could, in principle, be combined to build complex dynamical systems. The simplicity of our approach also suggests that natural molecular circuits may process some biomolecular oscillator outputs before they are applied downstream. PMID:26378119

  18. Biomolecular Detection employing the Interferometric Reflectance Imaging Sensor (IRIS)

    OpenAIRE

    Carlos A Lopez; George G Daaboul; Ahn, Sunmin; Reddington, Alexander P.; Monroe, Margo R.; Zhang, Xirui; Irani, Rostem J.; Yu, Chunxiao; Genco, Caroline A.; Cretich, Marina; Chiari, Marcella; Goldberg, Bennett B.; Connor, John H.; Ünlü, M. Selim

    2011-01-01

    The sensitive measurement of biomolecular interactions has use in many fields and industries such as basic biology and microbiology, environmental/agricultural/biodefense monitoring, nanobiotechnology, and more. For diagnostic applications, monitoring (detecting) the presence, absence, or abnormal expression of targeted proteomic or genomic biomarkers found in patient samples can be used to determine treatment approaches or therapy efficacy. In the research arena, information on molecular aff...

  19. Deterministic characterization of phase noise in biomolecular oscillators

    International Nuclear Information System (INIS)

    On top of the many external perturbations, cellular oscillators also face intrinsic perturbations due the randomness of chemical kinetics. Biomolecular oscillators, distinct in their parameter sets or distinct in their architecture, show different resilience with respect to such intrinsic perturbations. Assessing this resilience can be done by ensemble stochastic simulations. These are computationally costly and do not permit further insights into the mechanistic cause of the observed resilience. For reaction systems operating at a steady state, the linear noise approximation (LNA) can be used to determine the effect of molecular noise. Here we show that methods based on LNA fail for oscillatory systems and we propose an alternative ansatz. It yields an asymptotic expression for the phase diffusion coefficient of stochastic oscillators. Moreover, it allows us to single out the noise contribution of every reaction in an oscillatory system. We test the approach on the one-loop model of the Drosophila circadian clock. Our results are consistent with those obtained through stochastic simulations with a gain in computational efficiency of about three orders of magnitude

  20. 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...

  1. Biomolecular structure refinement using the GROMOS simulation software

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jozica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology ETH, Laboratory of Physical Chemistry (Switzerland)

    2011-11-15

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, {sup 3}J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  2. [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. PMID:26647577

  3. Microwave spectroscopy of biomolecular building blocks.

    Science.gov (United States)

    Alonso, José L; López, Juan C

    2015-01-01

    Microwave spectroscopy, considered as the most definitive gas phase structural probe, is able to distinguish between different conformational structures of a molecule, because they have unique spectroscopic constants and give rise to distinct individual rotational spectra.Previously, application of this technique was limited to molecular specimens possessing appreciable vapor pressures, thus discarding the possibility of studying many other molecules of biological importance, in particular those with high melting points, which had a tendency to undergo thermal reactions, and ultimately degradation, upon heating.Nowadays, the combination of laser ablation with Fourier transform microwave spectroscopy techniques, in supersonic jets, has enabled the gas-phase study of such systems. In this chapter, these techniques, including broadband spectroscopy, as well as results of their application into the study of the conformational panorama and structure of biomolecular building blocks, such as amino acids, nucleic bases, and monosaccharides, are briefly discussed, and with them, the tools for conformational assignation - rotational constants, nuclear quadrupole coupling interaction, and dipole moment. PMID:25721775

  4. Integrated Spintronic Platforms for Biomolecular Recognition Detection

    Science.gov (United States)

    Martins, V. C.; Cardoso, F. A.; Loureiro, J.; Mercier, M.; Germano, J.; Cardoso, S.; Ferreira, R.; Fonseca, L. P.; Sousa, L.; Piedade, M. S.; Freitas, P. P.

    2008-06-01

    This paper covers recent developments in magnetoresistive based biochip platforms fabricated at INESC-MN, and their application to the detection and quantification of pathogenic waterborn microorganisms in water samples for human consumption. Such platforms are intended to give response to the increasing concern related to microbial contaminated water sources. The presented results concern the development of biological active DNA chips and protein chips and the demonstration of the detection capability of the present platforms. Two platforms are described, one including spintronic sensors only (spin-valve based or magnetic tunnel junction based), and the other, a fully scalable platform where each probe site consists of a MTJ in series with a thin film diode (TFD). Two microfluidic systems are described, for cell separation and concentration, and finally, the read out and control integrated electronics are described, allowing the realization of bioassays with a portable point of care unit. The present platforms already allow the detection of complementary biomolecular target recognition with 1 pM concentration.

  5. 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.

  6. 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.

  7. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

    Science.gov (United States)

    Thibault, J C; Roe, D R; Eilbeck, K; Cheatham Iii, T E; Facelli, J C

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations. PMID:26387907

  8. Flourescence from Gas-Phase Biomolecular Ions

    DEFF Research Database (Denmark)

    Nielsen, Steen Brøndsted

    2013-01-01

    This chapter deals with measurements of fluorescence from electronically excited biomolecular ions where there are no interactions with an external environment. Biomolecules with no natural fluorophores are labelled with a dye for such experiments. First, some of the advantages, but also difficul...

  9. Amplified vibrational circular dichroism as a probe of local biomolecular structure.

    Science.gov (United States)

    Domingos, Sérgio R; Huerta-Viga, Adriana; Baij, Lambert; Amirjalayer, Saeed; Dunnebier, Dorien A E; Walters, Annemarie J C; Finger, Markus; Nafie, Laurence A; de Bruin, Bas; Buma, Wybren Jan; Woutersen, Sander

    2014-03-01

    We show that the VCD signal intensities of amino acids and oligopeptides can be enhanced by up to 2 orders of magnitude by coupling them to a paramagnetic metal ion. If the redox state of the metal ion is changed from paramagnetic to diamagnetic the VCD amplification vanishes completely. From this observation and from complementary quantum-chemical calculations we conclude that the observed VCD amplification finds its origin in vibronic coupling with low-lying electronic states. We find that the enhancement factor is strongly mode dependent and that it is determined by the distance between the oscillator and the paramagnetic metal ion. This localized character of the VCD amplification provides a unique tool to specifically probe the local structure surrounding a paramagnetic ion and to zoom in on such local structure within larger biomolecular systems. PMID:24506134

  10. 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

  11. 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

  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. 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.

  14. 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.

  15. Coassembly of aromatic dipeptides into biomolecular necklaces.

    Science.gov (United States)

    Yuran, Sivan; Razvag, Yair; Reches, Meital

    2012-11-27

    This paper describes the formation of complex peptide-based structures by the coassembly of two simple peptides, the diphenylalanine peptide and its tert-butyl dicarbonate (Boc) protected analogue. Each of these peptides can self-assemble into a distinct architecture: the diphenylalanine peptide into tubular structures and its analogue into spheres. Integrated together, these peptides coassemble into a construction of beaded strings, where spherical assemblies are connected by elongated elements. Electron and scanning force microscopy demonstrated the morphology of these structures, which we termed "biomolecular necklaces". Additional experiments indicated the reversibility of the coassembly process and the stability of the structures. Furthermore, we suggest a possible mechanism of formation for the biomolecular necklaces. Our suggestion is based on the necklace model for polyelectrolyte chains, which proposes that a necklace structure appears as a result of counterion condensation on the backbone of a polyelectrolyte. Overall, the approach of coassembly, demonstrated using aromatic peptides, can be adapted to any peptides and may lead to the development and discovery of new self-assembled architectures formed by peptides and other biomolecules. PMID:23061818

  16. Integration of biomolecular logic gates with field-effect transducers

    International Nuclear Information System (INIS)

    Highlights: → Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. → The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. → Logic gates were activated by different combinations of chemical inputs (analytes). → The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO2-Ta2O5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta2O5) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  17. Evaluation of stochastic effects on biomolecular networks using the generalised Nyquist stability criterion

    OpenAIRE

    Kim, J; Bates, D. G.; Postlethwaite, I.

    2008-01-01

    Abstract—Stochastic differential equations are now commonly used to model biomolecular networks in systems biology, and much recent research has been devoted to the development of methods to analyse their stability properties. Stability analysis of such systems may be performed using the Laplace transform, which requires the calculation of the exponential matrix involving time symbolically. However, the calculation of the symbolic exponential matrix is not feasible for problems of even mod...

  18. Ensemble based convergence assessment of biomolecular trajectories

    CERN Document Server

    Lyman, E; Lyman, Edward; Zuckerman, Daniel M.

    2006-01-01

    Assessing the convergence of a biomolecular simulation is an essential part of any computational investigation. This is because many important quantities (e.g., free energy differences) depend on the relative populations of different conformers; insufficient convergence translates into systematic errors. Here we present a simple method to self-consistently assess the convergence of a simulation. Standard clustering methods first generate a set of reference structures to any desired precision. The trajectory is then classified by proximity to the reference structures, yielding a one-dimensional histogram of structurally distinct populations. Comparing ensembles of different trajectories (or different parts of the same trajectory) built with the same reference structures provides a sensitive, quantitative measure of convergence. Please note: this is a preliminary manuscript, and should be read as such. Comments are most welcome, especially regarding pertinent prior work.

  19. Micro- and nanodevices integrated with biomolecular probes.

    Science.gov (United States)

    Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A

    2015-12-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. PMID:26363089

  20. Micro- and nanodevices integrated with biomolecular probes

    Science.gov (United States)

    Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A.

    2016-01-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. PMID:26363089

  1. 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.

  2. Biomolecular Self-Defense and Futility of High-Specificity Therapeutic Targeting

    OpenAIRE

    Simon Rosenfeld

    2011-01-01

    Robustness has been long recognized to be a distinctive property of living entities. While a reasonably wide consensus has been achieved regarding the conceptual meaning of robustness, the biomolecular mechanisms underlying this systemic property are still open to many unresolved questions. The goal of this paper is to provide an overview of existing approaches to characterization of robustness in mathematically sound terms. The concept of robustness is discussed in various contexts including...

  3. Biomolecular surface construction by PDE transform.

    Science.gov (United States)

    Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei

    2012-03-01

    This work proposes a new framework for the surface generation based on the partial differential equation (PDE) transform. The PDE transform has recently been introduced as a general approach for the mode decomposition of images, signals, and data. It relies on the use of arbitrarily high-order PDEs to achieve the time-frequency localization, control the spectral distribution, and regulate the spatial resolution. The present work provides a new variational derivation of high-order PDE transforms. The fast Fourier transform is utilized to accomplish the PDE transform so as to avoid stringent stability constraints in solving high-order PDEs. As a consequence, the time integration of high-order PDEs can be done efficiently with the fast Fourier transform. The present approach is validated with a variety of test examples in two-dimensional and three-dimensional settings. We explore the impact of the PDE transform parameters, such as the PDE order and propagation time, on the quality of resulting surfaces. Additionally, we utilize a set of 10 proteins to compare the computational efficiency of the present surface generation method and a standard approach in Cartesian meshes. Moreover, we analyze the present method by examining some benchmark indicators of biomolecular surface, that is, surface area, surface-enclosed volume, solvation free energy, and surface electrostatic potential. A test set of 13 protein molecules is used in the present investigation. The electrostatic analysis is carried out via the Poisson-Boltzmann equation model. To further demonstrate the utility of the present PDE transform-based surface method, we solve the Poisson-Nernst-Planck equations with a PDE transform surface of a protein. Second-order convergence is observed for the electrostatic potential and concentrations. Finally, to test the capability and efficiency of the present PDE transform-based surface generation method, we apply it to the construction of an excessively large biomolecule, a

  4. Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

    Science.gov (United States)

    Cole, Daniel J; Vilseck, Jonah Z; Tirado-Rives, Julian; Payne, Mike C; Jorgensen, William L

    2016-05-10

    Molecular mechanics force fields, which are commonly used in biomolecular modeling and computer-aided drug design, typically treat nonbonded interactions using a limited library of empirical parameters that are developed for small molecules. This approach does not account for polarization in larger molecules or proteins, and the parametrization process is labor-intensive. Using linear-scaling density functional theory and atoms-in-molecule electron density partitioning, environment-specific charges and Lennard-Jones parameters are derived directly from quantum mechanical calculations for use in biomolecular modeling of organic and biomolecular systems. The proposed methods significantly reduce the number of empirical parameters needed to construct molecular mechanics force fields, naturally include polarization effects in charge and Lennard-Jones parameters, and scale well to systems comprised of thousands of atoms, including proteins. The feasibility and benefits of this approach are demonstrated by computing free energies of hydration, properties of pure liquids, and the relative binding free energies of indole and benzofuran to the L99A mutant of T4 lysozyme. PMID:27057643

  5. 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

  6. 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

    2016-01-01

    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. PMID:27506964

  7. 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. PMID:23893064

  8. ssDNA-Functionalized Nanoceria: A Redox-Active Aptaswitch for Biomolecular Recognition.

    Science.gov (United States)

    Bülbül, Gonca; Hayat, Akhtar; Andreescu, Silvana

    2016-04-01

    Quantification of biomolecular binding events is a critical step for the development of biorecognition assays for diagnostics and therapeutic applications. This paper reports the design of redox-active switches based on aptamer conjugated nanoceria for detection and quantification of biomolecular recognition. It is shown that the conformational transition state of the aptamer on nanoceria, combined with the redox properties of these particles can be used to create surface based structure switchable aptasensing platforms. Changes in the redox properties at the nanoceria surface upon binding of the ssDNA and its target analyte enables rapid and highly sensitive measurement of biomolecular interactions. This concept is demonstrated as a general applicable method to the colorimetric detection of DNA binding events. An example of a nanoceria aptaswitch for the colorimetric sensing of Ochratoxin A (OTA) and applicability to other targets is provided. The system can sensitively and selectivity detect as low as 0.15 × 10(-9) m OTA. This novel assay is simple in design and does not involve oligonucleotide labeling or elaborate nanoparticle modification steps. The proposed mechanism discovered here opens up a new way of designing optical sensing methods based on aptamer recognition. This approach can be broadly applicable to many bimolecular recognition processes and related applications. PMID:26844813

  9. Self-assembling biomolecular catalysts for hydrogen production

    Science.gov (United States)

    Jordan, Paul C.; Patterson, Dustin P.; Saboda, Kendall N.; Edwards, Ethan J.; Miettinen, Heini M.; Basu, Gautam; Thielges, Megan C.; Douglas, Trevor

    2016-02-01

    The chemistry of highly evolved protein-based compartments has inspired the design of new catalytically active materials that self-assemble from biological components. A frontier of this biodesign is the potential to contribute new catalytic systems for the production of sustainable fuels, such as hydrogen. Here, we show the encapsulation and protection of an active hydrogen-producing and oxygen-tolerant [NiFe]-hydrogenase, sequestered within the capsid of the bacteriophage P22 through directed self-assembly. We co-opted Escherichia coli for biomolecular synthesis and assembly of this nanomaterial by expressing and maturing the EcHyd-1 hydrogenase prior to expression of the P22 coat protein, which subsequently self assembles. By probing the infrared spectroscopic signatures and catalytic activity of the engineered material, we demonstrate that the capsid provides stability and protection to the hydrogenase cargo. These results illustrate how combining biological function with directed supramolecular self-assembly can be used to create new materials for sustainable catalysis.

  10. Function of Amphiphilic Biomolecular Machines: Elastic Protein-based Polymers

    Science.gov (United States)

    Urry, Dan W.

    2000-03-01

    Elastic protein-based polymers function as biomolecular machines due to inverse temperature transitions of hydrophobic folding and assembly. The transitions occur either on raising the temperature from below to above the transition temperature, Tt, or on isothermally lowering Tt from above to below an operating temperature. The inverse temperature transition involves a decrease in entropy of the polymer component of the system on raising the temperature and a larger increase in solvent entropy on hydrophobic association. Tt depends on the quantity of hydrophobic hydration that undergoes transition to bulk water. Designed amphiphilic polymers perform free energy transductions involving the intensive variables of mechanical force, pressure, temperature, chemical potential, electrochemical potential and electromagnetic radiation and define a set of five axioms for their function as machines. The physical basis for these diverse energy conversions is competition for hydration between apolar (hydrophobic) and polar (e.g., charged) moieties. The effectiveness of these Tt-type entropic elastic protein-based machines is due to repeating peptide sequences that form regular, dynamic repeating structures and exhibit damping of backbone torsional oscillations on extension.

  11. A programmable biomolecular computing machine with bacterial phenotype output.

    Science.gov (United States)

    Kossoy, Elizaveta; Lavid, Noa; Soreni-Harari, Michal; Shoham, Yuval; Keinan, Ehud

    2007-07-23

    The main advantage of autonomous biomolecular computing devices over electronic computers is their ability to interact directly with biological systems. No interface is required since all components of molecular computers, including hardware, software, input, and output are molecules that interact in solution along a cascade of programmable chemical events. Here, we demonstrate for the first time that the output of a computation preduced by a molecular finite automaton can be a visible bacterial phenotype. Our 2-symbol-2-state finite automaton utilized linear double-stranded DNA inputs that were prepared by inserting a string of six base pair symbols into the lacZ gene on the pUC18 plasmid. The computation resulted in a circular plasmid that differed from the original pUC18 by either a 9 base pair (accepting state) or 11 base pair insert (unaccepting state) within the lacZ alpha region gene. Upon transformation and expression of the resultant plasmids in E. coli, the accepting state was represented by production of functional beta-galactosidase and formation of blue colonies on X-gal medium. In contrast, the unaccepting state was represented by white colonies due to a shift in the open reading frame of lacZ. PMID:17562552

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

    Science.gov (United States)

    Shapiro, Ehud

    2012-08-01

    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. PMID:22649583

  13. 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.

  14. The use of gold nanoparticle aggregation for DNA computing and logic-based biomolecular detection

    Energy Technology Data Exchange (ETDEWEB)

    Lee, In-Hee; Yang, Kyung-Ae; Zhang, Byoung-Tak [School of Computer Science and Engineering, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Lee, Ji-Hoon [Center for Bioinformation Technology, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul 151-742 (Korea, Republic of); Park, Ji-Yoon; Chai, Young Gyu [Division of Molecular and Life Sciences, Hanyang University, 1271 Sa-dong, Sangnok-gu, Ansan, Gyeonggi-do 426-791 (Korea, Republic of); Lee, Jae-Hoon [Fachgebiet Mikrobiologie und Genetik, Institut fuer Biotechnologie, Technische Universitaet Berlin, Gustav-Meyer Allee 25, D-13355 Berlin (Germany)], E-mail: btzhang@bi.snu.ac.kr

    2008-10-01

    The use of DNA molecules as a physical computational material has attracted much interest, especially in the area of DNA computing. DNAs are also useful for logical control and analysis of biological systems if efficient visualization methods are available. Here we present a quick and simple visualization technique that displays the results of the DNA computing process based on a colorimetric change induced by gold nanoparticle aggregation, and we apply it to the logic-based detection of biomolecules. Our results demonstrate its effectiveness in both DNA-based logical computation and logic-based biomolecular detection.

  15. 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

  16. Immunoenzymetic veterinary test - system for progesterone determination

    International Nuclear Information System (INIS)

    Radiopreparat enterprise specializes in manufacturing of radioisotope labeled compounds including radioimmunological test - systems for qualitative and quantitative determination of components of the blood and markers of a viruses. By the reason that the sensitivity of RIA is in 2 - 4 times less then sensitivity of immunoenzymetic test systems we have started the development this type of immunodiagnostic kits where as the detector acts the Peroxidase from horse redish instead of Iodine-125 as in RIA. One from the latest our developments is immunoenzymetic test system as the alternative variant of RIA for determination progesterone in blood of animals

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

    Science.gov (United States)

    Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto

    2013-01-01

    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. PMID:23437034

  18. 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.

  19. On coherent systems with fixed determinant

    OpenAIRE

    Grzegorczyk, I.; Newstead, P. E.

    2013-01-01

    Over the past 20 years, a great deal of work has been done on the moduli spaces of coherent systems on algebraic curves. Until recently, however, there has been very little work on the fixed determinant case, except for the special case of rank 2 and canonical determinant. This situation has changed due to two papers of B. Osserman, who has obtained lower bounds for the dimensions of the fixed determinant moduli spaces in some cases. Our object in this paper is to show that some of Osserman's...

  20. Buckling determination in reflected systems, program FLUXFIT

    International Nuclear Information System (INIS)

    An improvement in accuracy of determining radial and axial buckling from foil activation distributions measured in reflected cylindrical systems is given. resultant activities are fitted to radial and axial spatial functions derived from homogeneous diffusion theory. A Fortran program FLUXFIT based on the derived method is included. (author)

  1. The biomolecular and ultrastructural basis of epidermolysis bullosa:

    OpenAIRE

    Ciolan, Maria; Olariu, Liviu; Solovan, Caius

    2005-01-01

    Transmission electron microscopy, immunoelectron microscopy, immunofluorescence and antigenic mapping have improved our understanding of the dermo-epidermal junction. We have reviewed some ultrastructural and biomolecular aspects related to the dermo-epidermal junction. In part, they are implicated in the pathogenesis of a group of hereditary disorders characterized by skin fragility, collectively known as epidermolysis bullosa (EB). These disorders could benefit in the near future from a gen...

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

    OpenAIRE

    Shapiro, Ehud

    2012-01-01

    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 a...

  3. Dynamic Presentation of Immobilized Ligands Regulated through Biomolecular Recognition

    OpenAIRE

    Liu, Bo; Liu, Yang; Riesberg, Jeremiah J.; Shen, Wei

    2010-01-01

    To mimic the dynamic regulation of signaling ligands immobilized on extracellular matrices or on the surfaces of neighboring cells for guidance of cell behavior and fate selection, we have harnessed biomolecular recognition in combination with polymer engineering to create dynamic surfaces on which the accessibility of immobilized ligands to cell surface receptors can be reversibly interconverted under physiological conditions. The cell-adhesive RGD peptide is chosen as a model ligand. RGD is...

  4. 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.

  5. 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

  6. 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.

  7. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies

    International Nuclear Information System (INIS)

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.

  8. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies.

    Science.gov (United States)

    Zhou, Pei; Wagner, Gerhard

    2010-01-01

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR.We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs. PMID:19731047

  9. 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.

  10. 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.

  11. Spectral Color Effects in Biomolecular Interactions

    OpenAIRE

    Hecht, Christoph

    2007-01-01

    Persistent spectral hole burning has been employed to investigate various model systems of biological relevance upon their interactions with synthetic or intrinsic chromophores. The model chromophore thionin was assessed for its specific interactions with DNA oligonucleotides and cyclodextrin; the protein phycocyanin has been analyzed for its internal electrostatics. In all experiments spectral color effects have been found - changes of thermodynamic and electrostatic parameters within the sa...

  12. 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.

  13. 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

  14. ACEMD: Accelerating bio-molecular dynamics in the microsecond time-scale

    CERN Document Server

    Harvey, M J; De Fabritiis, G

    2009-01-01

    The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation program designed specifically for GPUs which is able to achieve supercomputing scale performance of 40 nanoseconds/day for all-atom protein systems with over 23,000 atoms. We illustrate the characteristics of the code, its validation and performance. We also run a microsecond-long trajectory for an all-atom molecular system in explicit TIP3P water on a single workstation computer equipped with just 3 GPUs. This performance on cost effective hardware allows ACEMD to reach microsecond timescales routinely with important implications in terms of scientific applications.

  15. Biomolecular self-defense and futility of high-specificity therapeutic targeting.

    Science.gov (United States)

    Rosenfeld, Simon

    2011-01-01

    Robustness has been long recognized to be a distinctive property of living entities. While a reasonably wide consensus has been achieved regarding the conceptual meaning of robustness, the biomolecular mechanisms underlying this systemic property are still open to many unresolved questions. The goal of this paper is to provide an overview of existing approaches to characterization of robustness in mathematically sound terms. The concept of robustness is discussed in various contexts including network vulnerability, nonlinear dynamic stability, and self-organization. The second goal is to discuss the implications of biological robustness for individual-target therapeutics and possible strategies for outsmarting drug resistance arising from it. Special attention is paid to the concept of swarm intelligence, a well studied mechanism of self-organization in natural, societal and artificial systems. It is hypothesized that swarm intelligence is the key to understanding the emergent property of chemoresistance. PMID:22272063

  16. 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.

  17. Enhanced semiempirical QM methods for biomolecular interactions

    Directory of Open Access Journals (Sweden)

    Nusret Duygu Yilmazer

    2015-01-01

    Full Text Available Recent successes and failures of the application of ‘enhanced’ semiempirical QM (SQM methods are reviewed in the light of the benefits and backdraws of adding dispersion (D and hydrogen-bond (H correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D, while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.

  18. 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.

  19. Piezoelectric tuning fork biosensors for the quantitative measurement of biomolecular interactions

    Science.gov (United States)

    Gonzalez, Laura; Rodrigues, Mafalda; Benito, Angel Maria; Pérez-García, Lluïsa; Puig-Vidal, Manel; Otero, Jorge

    2015-12-01

    The quantitative measurement of biomolecular interactions is of great interest in molecular biology. Atomic force microscopy (AFM) has proved its capacity to act as a biosensor and determine the affinity between biomolecules of interest. Nevertheless, the detection scheme presents certain limitations when it comes to developing a compact biosensor. Recently, piezoelectric quartz tuning forks (QTFs) have been used as laser-free detection sensors for AFM. However, only a few studies along these lines have considered soft biological samples, and even fewer constitute quantified molecular recognition experiments. Here, we demonstrate the capacity of QTF probes to perform specific interaction measurements between biotin-streptavidin complexes in buffer solution. We propose in this paper a variant of dynamic force spectroscopy based on representing adhesion energies E (aJ) against pulling rates v (nm s-1). Our results are compared with conventional AFM measurements and show the great potential of these sensors in molecular interaction studies.

  20. Near-infrared fluorophores as biomolecular probes

    Science.gov (United States)

    Patonay, Gabor; Beckford, Garfield; Strekowski, Lucjan; Henary, Maged; Merid, Yonathan

    2010-02-01

    Near-Infrared (NIR) fluorescence has been valuable in analytical and bioanalytical chemistry. NIR probes and labels have been used for several applications, including hydrophobicity of protein binding sites, DNA sequencing, immunoassays, CE separations, etc. The NIR region (700-1100 nm) has advantages for the spectroscopist due to the inherently lower background interference from the biological matrix and the high molar absorptivities of NIR chromophores. During the studies we report here several NIR dyes were prepared to determine the role of the hydrophobicity of NIR dyes and their charge in binding to amino acids and proteins, e.g., serum albumins. We synthesized NIR dye homologs containing the same chromophore but substituents of varying hydrophobicity. Hydrophobic moieties were represented by alkyl and aryl groups. These NIR dyes of varying hydrophobicity exhibited varying degrees of H-aggregation in aqueous solution indicating that the degree of H-aggregation could be used as an indicator to predict binding characteristics to serum albumins. In order to understand what factors may be important in the binding process, spectral behavior of these varying hydrophobicity dyes were examined in the presence of amino acids. Typical dye structures that exhibit large binding constants to biomolecules were compared in order to optimize applications utilizing non-covalent interactions.

  1. Cellular automata modelling of biomolecular networks dynamics.

    Science.gov (United States)

    Bonchev, D; Thomas, S; Apte, A; Kier, L B

    2010-01-01

    The modelling of biological systems dynamics is traditionally performed by ordinary differential equations (ODEs). When dealing with intracellular networks of genes, proteins and metabolites, however, this approach is hindered by network complexity and the lack of experimental kinetic parameters. This opened the field for other modelling techniques, such as cellular automata (CA) and agent-based modelling (ABM). This article reviews this emerging field of studies on network dynamics in molecular biology. The basics of the CA technique are discussed along with an extensive list of related software and websites. The application of CA to networks of biochemical reactions is exemplified in detail by the case studies of the mitogen-activated protein kinase (MAPK) signalling pathway, the FAS-ligand (FASL)-induced and Bcl-2-related apoptosis. The potential of the CA method to model basic pathways patterns, to identify ways to control pathway dynamics and to help in generating strategies to fight with cancer is demonstrated. The different line of CA applications presented includes the search for the best-performing network motifs, an analysis of importance for effective intracellular signalling and pathway cross-talk. PMID:20373215

  2. Biomolecular tracing using long-lived isotopes

    International Nuclear Information System (INIS)

    Accelerator mass spectrometry (AMS) was developed over the past 15 years as an essential tool for detecting long-lived, cosmogenic radio-isotopes in the earth and space sciences. We apply this technology to the measurement of chemical kinetics, primarily in biomedical systems, which had heretofore employed short-lived isotopes and/or long counting times to quantify radio-isotopic labels. AMS provides detection efficiencies of ∼ 1%, 103 to 106 better than decay-counting. Long-lived isotopes are used and detected with AMS at concentrations which reduce sample size, chemical dose, radiation safety hazards and radiolysis. We measure 3H, 7,1OBe, 14C, 26Al, 36CI, 41Ca and 129I, but most of our current program uses 14C. Initial experiments involved research on the genotoxicity of mutagens in cooked foods and reversible binding of compounds to antibodies. Through collaborations, we apply AMS detection to research in carcinogenesis, pharmacokinetics of toxins, elemental metabolism, distribution of topical medications and nutrition

  3. Protein hydrogels with engineered biomolecular recognition

    Science.gov (United States)

    Mi, Lixin

    water soluble and swelling. The RGD cell adhesion tripeptide has been inserted into the polyelectrolyte region by site-directed mutagenesis. Two dimensional human foreskin fibroblast cultures have shown that the RGD-containing protein surface is bioactive in promoting cell attachment, cell signaling, and cytoskeleton organization. The protein and the cell recognize and interact at molecular level. Collectively, these findings indicate that this bioactive protein hydrogel system is a promising biomaterial for mammalian cell culture. This research may provide insights for the rational development of bioactive ECM for specific cell and tissue engineering applications.

  4. 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.

  5. Biomolecular interaction analysis for carbon nanotubes and for biocompatibility prediction.

    Science.gov (United States)

    Chen, Xiaoping; Fang, Jinzhang; Cheng, Yun; Zheng, Jianhui; Zhang, Jingjing; Chen, Tao; Ruan, Benfang Helen

    2016-07-15

    The interactions between carbon nanotubes (CNTs) and biologics have been commonly studied by various microscopy and spectroscopy methods. We tried biomolecular interaction analysis to measure the kinetic interactions between proteins and CNTs. The analysis demonstrated that wheat germ agglutinin (WGA) and other proteins have high affinity toward carboxylated CNT (f-MWCNT) but essentially no binding to normal CNT (p-MWCNT). The binding of f-MWCNT-protein showed dose dependence, and the observed kinetic constants were in the range of 10(-9) to 10(-11) M with very small off-rates (10(-3) to 10(-7) s(-1)), indicating a relatively tight and stable f-MWCNT-protein complex formation. Interestingly in hemolysis assay, p-MWCNT showed good biocompatibility, f-MWCNT caused 30% hemolysis, but WGA-coated f-MWCNT did not show hemolysis. Furthermore, the f-MWCNT-WGA complex demonstrated enhanced cytotoxicity toward cancer cells, perhaps through the glycoproteins expressed on the cells' surface. Taken together, biomolecular interaction analysis is a precise method that might be useful in evaluating the binding affinity of biologics to CNTs and in predicting biological actions. PMID:27108187

  6. 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 ...

  7. 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).

  8. A program to calculate non-bonded interaction energy in biomolecular aggregates.

    Science.gov (United States)

    Sundaram, K; Prasad, C V

    1982-02-01

    This paper describes a program to calculate intermolecular as well as intramolecular electronic potential energy resulting from non-bonded interactions. The underlying theory is obtained by the application of Rayleigh-Schroedinger perturbation theory to non-overlap regions of a molecular system. The rigorous theoretical expressions for the energy terms are simplified by approximations consistent with those commonly employed in semi-empirical molecular orbital theories. The program is particularly suited for the study of biomolecular assemblies, and in situations where insight into contributions to total energy from various component interaction types is desired. The inclusion of the non-additive dispersion effects in this approach makes it especially interesting for the study of cooperative phenomena in the light of a recent finding [1]. PMID:7067416

  9. 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...

  10. Minimal metabolic pathway structure is consistent with associated biomolecular interactions.

    Science.gov (United States)

    Bordbar, Aarash; Nagarajan, Harish; Lewis, Nathan E; Latif, Haythem; Ebrahim, Ali; Federowicz, Stephen; Schellenberger, Jan; Palsson, Bernhard O

    2014-01-01

    Pathways are a universal paradigm for functionally describing cellular processes. Even though advances in high-throughput data generation have transformed biology, the core of our biological understanding, and hence data interpretation, is still predicated on human-defined pathways. Here, we introduce an unbiased, pathway structure for genome-scale metabolic networks defined based on principles of parsimony that do not mimic canonical human-defined textbook pathways. Instead, these minimal pathways better describe multiple independent pathway-associated biomolecular interaction datasets suggesting a functional organization for metabolism based on parsimonious use of cellular components. We use the inherent predictive capability of these pathways to experimentally discover novel transcriptional regulatory interactions in Escherichia coli metabolism for three transcription factors, effectively doubling the known regulatory roles for Nac and MntR. This study suggests an underlying and fundamental principle in the evolutionary selection of pathway structures; namely, that pathways may be minimal, independent, and segregated. PMID:24987116

  11. 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.

  12. 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.

  13. Perspective: Markov models for long-timescale biomolecular dynamics

    International Nuclear Information System (INIS)

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics

  14. Nanopatterned structures for biomolecular analysis toward genomic and proteomic applications

    Science.gov (United States)

    Chou, Chia-Fu; Gu, Jian; Wei, Qihuo; Liu, Yingjie; Gupta, Ravi; Nishio, Takeyoshi; Zenhausern, Frederic

    2005-01-01

    We report our fabrication of nanoscale devices using electron beam and nanoimprint lithography (NIL). We focus our study in the emerging fields of NIL, nanophotonics and nanobiotechnology and give a few examples as to how these nanodevices may be applied toward genomic and proteomic applications for molecular analysis. The examples include reverse NIL-fabricated nanofluidic channels for DNA stretching, nanoscale molecular traps constructed from dielectric constrictions for DNA or protein focusing by dielectrophoresis, multi-layer nanoburger and nanoburger multiplets for optimized surface-plasma enhanced Raman scattering for protein detection, and biomolecular motor-based nanosystems. The development of advanced nanopatterning techniques promises reliable and high-throughput manufacturing of nanodevices which could impact significantly on the areas of genomics, proteomics, drug discovery and molecular clinical diagnostics.

  15. Perspective: Markov Models for Long-Timescale Biomolecular Dynamics

    CERN Document Server

    Schwantes, Christian R; Pande, Vijay S

    2014-01-01

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.

  16. Wear determination in braking systems by radioisotopes

    International Nuclear Information System (INIS)

    Friction and wear behaviour of friction couples has been tested applying loads and sliding speeds. The determination was carried out by direct measurements of the lining material and by surface activation of the opposite material with protons. The application limits of several braking materials could be determined and compared

  17. 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.

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

    International Nuclear Information System (INIS)

    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. (report on progress)

  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. 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

    International Nuclear Information System (INIS)

    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

  1. Photodamage and the importance of photoprotection in biomolecular-powered device applications.

    Science.gov (United States)

    Vandelinder, Virginia; Bachand, George D

    2014-01-01

    In recent years, an enhanced understanding of the mechanisms underlying photobleaching and photoblinking of fluorescent dyes has led to improved photoprotection strategies, such as reducing and oxidizing systems (ROXS) that reduce blinking and oxygen scavenging systems to reduce bleaching. Excitation of fluorescent dyes can also result in damage to catalytic proteins (e.g., biomolecular motors), affecting the performance of integrated devices. Here, we characterized the motility of microtubules driven by kinesin motor proteins using various photoprotection strategies, including a microfluidic deoxygenation device. Impaired motility of microtubules was observed at high excitation intensities in the absence of photoprotection as well as in the presence of an enzymatic oxygen scavenging system. In contrast, using a polydimethylsiloxane (PDMS) microfluidic deoxygenation device and ROXS, not only were the fluorophores slower to bleach but also moving the velocity and fraction of microtubules over time remained unaffected even at high excitation intensities. Further, we demonstrate the importance of photoprotection by examining the effect of photodamage on the behavior of a switchable mutant of kinesin. Overall, these results demonstrate that improved photoprotection strategies may have a profound impact on functional fluorescently labeled biomolecules in integrated devices. PMID:24350711

  2. SWISS-PROT: connecting biomolecular knowledge via a protein database.

    Science.gov (United States)

    Gasteiger, E; Jung, E; Bairoch, A

    2001-07-01

    With the explosive growth of biological data, the development of new means of data storage was needed. More and more often biological information is no longer published in the conventional way via a publication in a scientific journal, but only deposited into a database. In the last two decades these databases have become essential tools for researchers in biological sciences. Biological databases can be classified according to the type of information they contain. There are basically three types of sequence-related databases (nucleic acid sequences, protein sequences and protein tertiary structures) as well as various specialized data collections. It is important to provide the users of biomolecular databases with a degree of integration between these databases as by nature all of these databases are connected in a scientific sense and each one of them is an important piece to biological complexity. In this review we will highlight our effort in connecting biological information as demonstrated in the SWISS-PROT protein database. PMID:11488411

  3. Determination of a radioactive waste classification system

    Energy Technology Data Exchange (ETDEWEB)

    Cohen, J.J.; King, W.C.

    1978-03-01

    Several classification systems for radioactive wastes are reviewed and a system is developed that provides guidance on disposition of the waste. The system has three classes: high-level waste (HLW), which requires complete isolation from the biosphere for extended time periods; low-level waste (LLW), which requires containment for shorter periods; and innocuous waste (essentially nonradioactive), which may be disposed of by conventional means. The LLW/innocuous waste interface was not defined in this study. Reasonably conservative analytical scenarios were used to calculate that HLW/LLW interface level which would ensure compliance with the radiological exposure guidelines of 0.5 rem/y maximum exposure for a few isolated individuals and 0.005 rem/y for large population groups. The recommended HLW/LLW interface level for /sup 239/Pu or mixed transuranic waste is 1.0 ..mu..Ci/cm/sup 3/ of waste. Levels for other radionuclides are based upon a risk equivalent to this level. A cost-benefit analysis in accordance with as low as reasonably achievable (ALARA) and National Environmental Protection Act (NEPA) guidance indicates that further reduction of this HLW/LLL interface level would entail marginal costs greater than $10/sup 8/ per man-rem of dose avoided. The environmental effects considered were limited to those involving human exposure to radioactivity.

  4. Determination of a radioactive waste classification system

    International Nuclear Information System (INIS)

    Several classification systems for radioactive wastes are reviewed and a system is developed that provides guidance on disposition of the waste. The system has three classes: high-level waste (HLW), which requires complete isolation from the biosphere for extended time periods; low-level waste (LLW), which requires containment for shorter periods; and innocuous waste (essentially nonradioactive), which may be disposed of by conventional means. The LLW/innocuous waste interface was not defined in this study. Reasonably conservative analytical scenarios were used to calculate that HLW/LLW interface level which would ensure compliance with the radiological exposure guidelines of 0.5 rem/y maximum exposure for a few isolated individuals and 0.005 rem/y for large population groups. The recommended HLW/LLW interface level for 239Pu or mixed transuranic waste is 1.0 μCi/cm3 of waste. Levels for other radionuclides are based upon a risk equivalent to this level. A cost-benefit analysis in accordance with as low as reasonably achievable (ALARA) and National Environmental Protection Act (NEPA) guidance indicates that further reduction of this HLW/LLL interface level would entail marginal costs greater than $108 per man-rem of dose avoided. The environmental effects considered were limited to those involving human exposure to radioactivity

  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. Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads

    Science.gov (United States)

    Stone, John E.; Hallock, Michael J.; Phillips, James C.; Peterson, Joseph R.; Luthey-Schulten, Zaida; Schulten, Klaus

    2016-01-01

    Many of the continuing scientific advances achieved through computational biology are predicated on the availability of ongoing increases in computational power required for detailed simulation and analysis of cellular processes on biologically-relevant timescales. A critical challenge facing the development of future exascale supercomputer systems is the development of new computing hardware and associated scientific applications that dramatically improve upon the energy efficiency of existing solutions, while providing increased simulation, analysis, and visualization performance. Mobile computing platforms have recently become powerful enough to support interactive molecular visualization tasks that were previously only possible on laptops and workstations, creating future opportunities for their convenient use for meetings, remote collaboration, and as head mounted displays for immersive stereoscopic viewing. We describe early experiences adapting several biomolecular simulation and analysis applications for emerging heterogeneous computing platforms that combine power-efficient system-on-chip multi-core CPUs with high-performance massively parallel GPUs. We present low-cost power monitoring instrumentation that provides sufficient temporal resolution to evaluate the power consumption of individual CPU algorithms and GPU kernels. We compare the performance and energy efficiency of scientific applications running on emerging platforms with results obtained on traditional platforms, identify hardware and algorithmic performance bottlenecks that affect the usability of these platforms, and describe avenues for improving both the hardware and applications in pursuit of the needs of molecular modeling tasks on mobile devices and future exascale computers.

  7. Duplication and Divergence Effect on Network Motifs in Undirected Bio-Molecular Networks.

    Science.gov (United States)

    Pei Wang; Jinhu Lu; Xinghuo Yu; Zengrong Liu

    2015-06-01

    Duplication and divergence are two basic evolutionary mechanisms of bio-molecular networks. Real-world bio-molecular networks and their statistical characteristics can be well mimicked by artificial algorithms based on the two mechanisms. Bio-molecular networks consist of network motifs, which act as building blocks of large-scale networks. A fundamental question is how network motifs are evolved from long time evolution and natural selection. By considering the effect of various duplication and divergence strategies, we find that the underlying duplication scheme of the real-world undirected bio-molecular networks would rather follow the anti-preference strategy than the random one. The anti-preference duplication mechanism and the dimerization processes can lead to the formation of various motifs, and robustly conserve proper quantities of motifs in the artificial networks as that in the real-world ones. Furthermore, the anti-preference mechanism and edge deletion divergence can robustly preserve the sparsity of the networks. The investigations reveal the possible evolutionary mechanisms of network motifs in real-world bio-molecular networks, and have potential implications in the design, synthesis and reengineering of biological networks for biomedical purpose. PMID:25203993

  8. Soft Supercharging of Biomolecular Ions in Electrospray Ionization Mass Spectrometry

    Science.gov (United States)

    Chingin, Konstantin; Xu, Ning; Chen, Huanwen

    2014-06-01

    The charge states of biomolecular ions in ESI-MS can be significantly increased by the addition of low-vapor supercharging (SC) reagents into the spraying solution. Despite the considerable interest from the community, the mechanistic aspects of SC are not well understood and are hotly debated. Arguments that denaturation accounts for the increased charging observed in proteins sprayed from aqueous solutions containing SC reagent have been published widely, but often with incomplete or ambiguous supporting data. In this work, we explored ESI MS charging and SC behavior of several biopolymers including proteins and DNA oligonucleotides. Analytes were ionized from 100 mM ammonium acetate (NH4Ac) aqueous buffer in both positive (ESI+) and negative (ESI-) ion modes. SC was induced either with m-NBA or by the elevated temperature of ESI capillary. For all the analytes studied we, found striking differences in the ESI MS response to these two modes of activation. The data suggest that activation with m-NBA results in more extensive analyte charging with lower degree of denaturation. When working solution with m-NBA was analyzed at elevated temperatures, the SC effect from m-NBA was neutralized. Instead, the net SC effect was similar to the SC effect achieved by thermal activation only. Overall, our observations indicate that SC reagents enhance ESI charging of biomolecules via distinctly different mechanism compared with the traditional approaches based on analyte denaturation. Instead, the data support the hypothesis that the SC phenomenon involves a direct interaction between a biopolymer and SC reagent occurring in evaporating ESI droplets.

  9. 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.

  10. 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. PMID:22247593

  11. Biomolecular environment, quantification, and intracellular interaction of multifunctional magnetic SERS nanoprobes.

    Science.gov (United States)

    Büchner, Tina; Drescher, Daniela; Merk, Virginia; Traub, Heike; Guttmann, Peter; Werner, Stephan; Jakubowski, Norbert; Schneider, Gerd; Kneipp, Janina

    2016-08-15

    Multifunctional composite nanoprobes consisting of iron oxide nanoparticles linked to silver and gold nanoparticles, Ag-Magnetite and Au-Magnetite, respectively, were introduced by endocytic uptake into cultured fibroblast cells. The cells containing the non-toxic nanoprobes were shown to be displaceable in an external magnetic field and can be manipulated in microfluidic channels. The distribution of the composite nanostructures that are contained in the endosomal system is discussed on the basis of surface-enhanced Raman scattering (SERS) mapping, quantitative laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) micromapping, and cryo soft X-ray tomography (cryo soft-XRT). Cryo soft-XRT of intact, vitrified cells reveals that the composite nanoprobes form intra-endosomal aggregates. The nanoprobes provide SERS signals from the biomolecular composition of their surface in the endosomal environment. The SERS data indicate the high stability of the nanoprobes and of their plasmonic properties in the harsh environment of endosomes and lysosomes. The spectra point at the molecular composition at the surface of the Ag-Magnetite and Au-Magnetite nanostructures that is very similar to that of other composite structures, but different from the composition of pure silver and gold SERS nanoprobes used for intracellular investigations. As shown by the LA-ICP-MS data, the uptake efficiency of the magnetite composites is approximately two to three times higher than that of the pure gold and silver nanoparticles. PMID:27353290

  12. 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...

  13. 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

    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...

  14. Multiple Features Based Approach to Extract Bio-molecular Event Triggers Using Conditional Random Field

    Directory of Open Access Journals (Sweden)

    Amit Majumder

    2012-11-01

    Full Text Available The purpose of Biomedical Natural Language Processing (BioNLP is to capture biomedical phenomena from textual data by extracting relevant entities, information and relations between biomedical entities (i.e. proteins and genes. In general, in most of the published papers, only binary relations were extracted. In a recent past, the focus is shifted towards extracting more complex relations in the form of bio-molecular events that may include several entities or other relations. In this paper we propose an approach that enables event trigger extraction of relatively complex bio-molecular events. We approach this problem as a detection of bio-molecular event trigger using the well-known algorithm, namely Conditional Random Field (CRF. We apply our experiments on development set. It shows the overall average recall, precision and F-measure values of 64.27504%, 69.97559% and 67.00429%, respectively for the event detection.

  15. From Correlation to Causality: Statistical Approaches to Learning Regulatory Relationships in Large-Scale Biomolecular Investigations.

    Science.gov (United States)

    Ness, Robert O; Sachs, Karen; Vitek, Olga

    2016-03-01

    Causal inference, the task of uncovering regulatory relationships between components of biomolecular pathways and networks, is a primary goal of many high-throughput investigations. Statistical associations between observed protein concentrations can suggest an enticing number of hypotheses regarding the underlying causal interactions, but when do such associations reflect the underlying causal biomolecular mechanisms? The goal of this perspective is to provide suggestions for causal inference in large-scale experiments, which utilize high-throughput technologies such as mass-spectrometry-based proteomics. We describe in nontechnical terms the pitfalls of inference in large data sets and suggest methods to overcome these pitfalls and reliably find regulatory associations. PMID:26731284

  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. Determination of mutual diffusion coefficients in quaternary alloy systems

    International Nuclear Information System (INIS)

    Procedures of experimental study of mutual diffusion in four-component system are developed, limit ratios for diffusion coefficients are found at the transition from four component system to three-component one and experimental check of some of these ratios is carried out. Concentrational dependence of complete matrix of outer diffusion coefficients in Fe-Cr-Ni-Co system is determined. Limit correlations for this system are checked up at cobalt concentration yielding to zero

  18. Alternative irradiation system for efficiency manganese bath determination

    International Nuclear Information System (INIS)

    The Manganese Sulphate Bath (MSB) is the main method used in most metrological laboratories to measure the neutron sources emission rate Q(t) . The MSB technique consists, basically, in dipping a neutron source in the center of a large tank (∼500 L) containing a concentrated aqueous solution of manganese sulphate. The neutron source emission rate is determined through the activity solution measurement produced by captured neutrons in manganese nuclei. In order to obtain the value of Q(t) it must be taken into account the detection system efficiency and still determine some corrections. The MSB system efficiency is usually determined by irradiating a solution sample from MSB system in a reactor or accelerator. This paper proposes an alternative irradiation system (Irradiation Bath), which works with a radionuclide neutron source and manganese sulphate solution volume for efficiency determination of MSB system. This irradiation system was designed by simulation with MCNP code, considering a californium neutron source in several manganese sulphate volumes and different neutron reflectors. The goal of this simulation was to determine the materials and dimensions of Irradiation Bath which will derive the maximum manganese neutron capture. Although the specific activated irradiated samples are less than those in reactors, the simulation results for optimized Irradiation Bath have showed a manganese neutron capture increase up to 100 times with dimensions less than 15 cm in diameter when it compared to manganese neutron capture in a MSB System whose diameter is about 100 cm . (author)

  19. Determination of eigenvalues of dynamical systems by symbolic computation

    Science.gov (United States)

    Howard, J. C.

    1982-01-01

    A symbolic computation technique for determining the eigenvalues of dynamical systems is described wherein algebraic operations, symbolic differentiation, matrix formulation and inversion, etc., can be performed on a digital computer equipped with a formula-manipulation compiler. An example is included that demonstrates the facility with which the system dynamics matrix and the control distribution matrix from the state space formulation of the equations of motion can be processed to obtain eigenvalue loci as a function of a system parameter. The example chosen to demonstrate the technique is a fourth-order system representing the longitudinal response of a DC 8 aircraft to elevator inputs. This simplified system has two dominant modes, one of which is lightly damped and the other well damped. The loci may be used to determine the value of the controlling parameter that satisfied design requirements. The results were obtained using the MACSYMA symbolic manipulation system.

  20. Optical Coherence Tomography and Biomolecular Imaging with Coherent Raman Scattering Microscopy

    DEFF Research Database (Denmark)

    Andersson-Engels, Stefan; Andersen, Peter E.

    2014-01-01

    The Special Section on Selected Topics in Biophotonics: Optical Coherence Tomography and Biomolecular Imaging with Coherent Raman Scattering Microscopy comprises two invited review papers and several contributed papers from the summer school Biophotonics ’13, as well as contributed papers within...

  1. Transition metal bioconjugates with an organometallic link between the metal and the biomolecular scaffold

    OpenAIRE

    Monney, Angèle; Albrecht, Martin

    2013-01-01

    This overview compiles recent advances in the synthesis and application of organometallic bioconjugates that comprise a metal–carbon linkage between the metal and the biomolecular scaffold. This specific area of bioorganometallic chemistry has been spurred by the discovery of naturally occurring bioorganometallic compounds and afforded organometallic bioconjugates from transition metals binding to amino acids, nucleic acids and other biomolecules. These artificial bioorganometallic compounds ...

  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. 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.

  4. Applicability of carbon and boron nitride nanotubes as biosensors: Effect of biomolecular adsorption on the transport properties of carbon and boron nitride nanotubes

    Science.gov (United States)

    Zhong, Xiaoliang; Mukhopadhyay, Saikat; Gowtham, S.; Pandey, Ravindra; Karna, Shashi P.

    2013-04-01

    The effect of molecular adsorption on the transport properties of single walled carbon and boron nitride nanotubes (CNTs and BNNTs) is investigated using density functional theory and non-equilibrium Green's function methods. The calculated I-V characteristics predict noticeable changes in the conductivity of semiconducting BNNTs due to physisorption of nucleic acid base molecules. Specifically, guanine which binds to the side wall of BNNT significantly enhances its conductivity by introducing conduction channels near the Fermi energy of the bioconjugated system. For metallic CNTs, a large background current masks relatively small changes in current due to the biomolecular adsorption. The results therefore suggest the suitability of BNNTs for biosensing applications.

  5. A GPS-Based Attitude Determination System for Small Satellites

    OpenAIRE

    Gershman, Daniel; Young, Kristopher; Kelsey, Anders; Eldad, Ofer; Rostoker, Jason; Mohiuddin, Shan; Cerruti, Alessandro; Peck, Mason

    2006-01-01

    This paper presents a novel, GPS-based attitude determination system (ADS). Carrier-phase differential GPS (CDGPS) accurate to within centimeters enables magnetometer-level pointing accuracy. Employing three GPS antennas allows for the determination of three independent baseline vectors, which can be combined to yield a precise attitude solution. Both simulation data for a satellite in LEO and terrestrial field test data suggest subcentimeter level accuracy, yielding an instantaneous pointing...

  6. Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

    Science.gov (United States)

    Yoo, Jejoong; Wilson, James; Aksimentiev, Aleksei

    2016-10-01

    Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular classical force fields AMBER and CHARMM by computing the osmotic pressure of model compounds and the free energy of DNA-DNA interactions. In the simulations performed using the two standard models, Ca(2+) ions are seen to form artificial clusters with chloride, acetate, and phosphate species; the osmotic pressure of CaAc2 and CaCl2 solutions is a small fraction of the experimental values for both force fields. Using the standard parameterization of Ca(2+) ions in the simulations of Ca(2+) -mediated DNA-DNA interactions leads to qualitatively wrong outcomes: both AMBER and CHARMM simulations suggest strong inter-DNA attraction whereas, in experiment, DNA molecules repel one another. The artificial attraction of Ca(2+) to DNA phosphate is strong enough to affect the direction of the electric field-driven translocation of DNA through a solid-state nanopore. To address these shortcomings of the standard Ca(2+) model, we introduce a custom model of a hydrated Ca(2+) ion and show that using our model brings the results of the above MD simulations in quantitative agreement with experiment. Our improved model of Ca(2+) can be readily applied to MD simulations of various biomolecular systems, including nucleic acids, proteins and lipid bilayer membranes. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 752-763, 2016. PMID:27144470

  7. A synergic simulation-optimization approach for analyzing biomolecular dynamics in living organisms.

    Science.gov (United States)

    Sadegh Zadeh, Kouroush

    2011-01-01

    A synergic duo simulation-optimization approach was developed and implemented to study protein-substrate dynamics and binding kinetics in living organisms. The forward problem is a system of several coupled nonlinear partial differential equations which, with a given set of kinetics and diffusion parameters, can provide not only the commonly used bleached area-averaged time series in fluorescence microscopy experiments but more informative full biomolecular/drug space-time series and can be successfully used to study dynamics of both Dirac and Gaussian fluorescence-labeled biomacromolecules in vivo. The incomplete Cholesky preconditioner was coupled with the finite difference discretization scheme and an adaptive time-stepping strategy to solve the forward problem. The proposed approach was validated with analytical as well as reference solutions and used to simulate dynamics of GFP-tagged glucocorticoid receptor (GFP-GR) in mouse cancer cell during a fluorescence recovery after photobleaching experiment. Model analysis indicates that the commonly practiced bleach spot-averaged time series is not an efficient approach to extract physiological information from the fluorescence microscopy protocols. It was recommended that experimental biophysicists should use full space-time series, resulting from experimental protocols, to study dynamics of biomacromolecules and drugs in living organisms. It was also concluded that in parameterization of biological mass transfer processes, setting the norm of the gradient of the penalty function at the solution to zero is not an efficient stopping rule to end the inverse algorithm. Theoreticians should use multi-criteria stopping rules to quantify model parameters by optimization. PMID:21106190

  8. Consumer Preferences Determine Resilience of Ecological-Economic Systems

    Directory of Open Access Journals (Sweden)

    Sebastian Strunz

    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.

  9. A system dynamics model to determine products mix

    OpenAIRE

    Mahtab Hajghasem; Payam Makvandi; Seyed Shahrooz Seyedi Hosseininia

    2014-01-01

    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 dyna...

  10. Determining energy production of CdTe photovoltaic system

    OpenAIRE

    Virtič, Peter; Šlamberger, Jan

    2015-01-01

    This paper presents a method for determining energy production of Cadmium-Telluride photovoltaic system, which has a different working performance than the most used Silicon photovoltaic systems. The main difference is sensitivity to the temperature and the solar irradiance. The CdTe cells are less sensitive to the temperature and in contrast to the Si Cells they have a higher efficiency at lower irradiance.

  11. Earth Observing System (EOS) real-time onboard orbit determination

    Science.gov (United States)

    Folta, David C.; Muller, Ron

    1993-01-01

    The paper describes the TDRSS Onboard Navigation System (TONS) selected by NASA/GSFC for the EOS-AM1 spacecraft as the baseline navigation system for real-time onboard orbit determination. Particular attention is given to the TONS algorithms and environmental models, the general design considerations, the algorithm implementation, and the required hardware. Results are presented of the covariance analysis for the nominal onboard and instrument requirements.

  12. STARSYS data messaging and geographic position determination system

    Science.gov (United States)

    Kaveeshwar, Ashok

    The STARSYS satellite system is a low earth orbit, 'little LEO' network of 24 'bent pipe' satellites designed to provide low cost data relay (store and forward) services as well as geographic position determination services. STARSYS is a joint venture of ST Systems Corporation (STX) and North American Collection and Location by Satellite (NACLS). This project which will operate in the 148-149.9 MHz/137-138 MHz bandwidths is based upon experience gained with the Argos environmental satellite project.

  13. Modular Attitude Determination and Control System for Small Satellites

    OpenAIRE

    Selby, Vaughn

    1990-01-01

    In order to meet the cost goals of small satellites, attitude determination and control problems must be solved using standardized components. Small satellite attitude control systems must feature performance, versatility, and above all, low cost Large, custom designed, high cost attitude control systems have no place in the small satellite community. A modular concept of attitude control is presented which will allow ambitious performance and cost goals to be attained. Basic building blocks ...

  14. Error Analysis of Determining Airplane Location by Global Positioning System

    OpenAIRE

    Hajiyev, Chingiz; Burat, Alper

    1999-01-01

    This paper studies the error analysis of determining airplane location by global positioning system (GPS) using statistical testing method. The Newton Rhapson method positions the airplane at the intersection point of four spheres. Absolute errors, relative errors and standard deviation have been calculated The results show that the positioning error of the airplane varies with the coordinates of GPS satellite and the airplane.

  15. Biomolecular Mechanisms of Pseudomonas aeruginosa and Escherichia coli Biofilm Formation

    Directory of Open Access Journals (Sweden)

    Garry Laverty

    2014-07-01

    Full Text Available Pseudomonas aeruginosa and Escherichia coli are the most prevalent Gram-negative biofilm forming medical device associated pathogens, particularly with respect to catheter associated urinary tract infections. In a similar manner to Gram-positive bacteria, Gram-negative biofilm formation is fundamentally determined by a series of steps outlined more fully in this review, namely adhesion, cellular aggregation, and the production of an extracellular polymeric matrix. More specifically this review will explore the biosynthesis and role of pili and flagella in Gram-negative adhesion and accumulation on surfaces in Pseudomonas aeruginosa and Escherichia coli. The process of biofilm maturation is compared and contrasted in both species, namely the production of the exopolysaccharides via the polysaccharide synthesis locus (Psl, pellicle Formation (Pel and alginic acid synthesis in Pseudomonas aeruginosa, and UDP-4-amino-4-deoxy-l-arabinose and colonic acid synthesis in Escherichia coli. An emphasis is placed on the importance of the LuxR homologue sdiA; the luxS/autoinducer-II; an autoinducer-III/epinephrine/norepinephrine and indole mediated Quorum sensing systems in enabling Gram-negative bacteria to adapt to their environments. The majority of Gram-negative biofilms consist of polysaccharides of a simple sugar structure (either homo- or heteropolysaccharides that provide an optimum environment for the survival and maturation of bacteria, allowing them to display increased resistance to antibiotics and predation.

  16. 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.

  17. 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.

  18. 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...

  19. Micromachining microcarrier-based biomolecular encoding for miniaturized and multiplexed immunoassay.

    Science.gov (United States)

    Zhi, Zheng-liang; Morita, Yasutaka; Hasan, Quamrul; Tamiya, Eiichi

    2003-08-15

    Micromachining techniques, which originated in the microelectronics industry, have been employed to manufacture microparticles bearing an engraved dot-type signature for biomolecular encoding. These metallic microstructures are photolithographically defined and manufactured in a highly reproducible manner. In addition, the code introduced on the particle face is a straightforward visible feature that is easily recognizable with the use of optical microscopy. The number of distinct codes theoretically could be many thousands, depending on the coding element numbers. Such microparticles are, thus, with appropriate surface organic functionalizations, ideal for encoding biomolecular libraries and serving as a platform for developing high-throughput multiplexed bioassay schemes based on suspension array technology. As proof of this statement, we demonstrated that encoded microparticles tagged with antibodies to human immunoglobulin classes are capable, using imaging detection as the interrogating approach, of high sensitivity and high specificity, as well as multiplexed detection of the respective antigens in a microliter-sample volume. PMID:14651038

  20. Theoretical models for the emergence of biomolecular homochirality

    Science.gov (United States)

    Walker, Sara Imari

    Little is known about the emergence of life from nonliving precursors. A key missing-piece is the origin of homochirality: nearly all life is characterized by exclusively dextrorotary sugars and levorotary amino acids. The research presented in this thesis addresses the challenge of uncovering mechanisms for chiral symmetry breaking in a prebiotic environment and implications for the origin of life on Earth. Expanding on a well-known model for chiral selection through polymerization, and modeling the spatiotemporal dynamics starting from near-racemic initial conditions, it is demonstrated that the net chirality of molecular building blocks grows with the longest polymer in the reaction network (of length N) with critical behavior for the onset of chiral asymmetry determined by the value of N. This surprising result indicates that significant chiral asymmetry occurs only for systems which permit growth of long polymers. Expanding on this work, the effects of environmental disturbances on the evolution of chirality in prebiotic reaction-diffusion networks are studied via the implementation of a stochastic spatiotemporal Langevin equation. The results show that environmental interactions can have significant impact on the evolution of prebiotic chirality: the history of prebiotic chirality is therefore interwoven with the Earths early environmental history in a mechanism we call punctuated chirality. This result establishes that the onset of homochirality is not an isolated phenomenon: chiral selection must occur in tandem with the transition from chemistry to biology, otherwise the prebiotic soup is unstable to environmental events. Addressing the challenge of understanding the role of chirality in the transition from non-life to life, the diffusive slowdown of reaction networks induced, for example, through tidal cycles or evaporating pools, is modeled. The results of this study demonstrate that such diffusive slowdown leads to the stabilization of homochiral

  1. 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...

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

    OpenAIRE

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

    2015-01-01

    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 pe...

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

    OpenAIRE

    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 c...

  4. Atomic force microscopy of self-assembled biomolecular structures and their interaction with metallic nanoparticles.

    OpenAIRE

    Gysemans, Maarten

    2009-01-01

    We applied AFM to study biomolecular wires, both out of interest in thei r biological functions and in the framework of nanotechnology based fabr ication. We have focused on two different kinds of protein wires: Insuli n fibrils and microtubules. Microtubules are an important constituent of the cytoskeleton and fulfill multiple vital functions in the cell. Insu lin fibrils on the other hand are amyloid fibrils without a clear biolog ical role, but with intriguing polymerization properties tha...

  5. The Shadow Map: A General Contact Definition for Capturing the Dynamics of Biomolecular Folding and Function

    OpenAIRE

    Jeffrey K Noel; Whitford, Paul C.; Onuchic, José N.

    2012-01-01

    Structure-based models (SBMs) are simplified models of the biomolecular dynamics that arise from funneled energy landscapes. We recently introduced an all-atom SBM that explicitly represents the atomic geometry of a biomolecule. While this initial study showed the robustness of the all-atom SBM Hamiltonian to changes in many of the energetic parameters, an important aspect, which has not been explored previously, is the definition of native interactions. In this study, we propose a general de...

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

    OpenAIRE

    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 arou...

  7. Affinity capillary electrophoresis and density functional theory employed for characterization of (bio)molecular interactions

    Czech Academy of Sciences Publication Activity Database

    Kašička, Václav; Ehala, Sille; Růžička, Martin; Dybal, Jiří; Toman, Petr

    Salzburg: Society of Analytical Chemistry, 2014. OR28. [ISC 2014. International Symposium on Chromatography /30./. 14.09.2014-18.09.2014, Salzburg] R&D Projects: GA ČR(CZ) GAP206/12/0453; GA ČR(CZ) GA13-17224S Institutional support: RVO:61388963 ; RVO:61389013 Keywords : affinity capillary electrophoresis * density functional theory * biomolecular complexes Subject RIV: CB - Analytical Chemistry, Separation

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

    OpenAIRE

    Hayward Steven; Stocks Matthew B; Laycock Stephen D

    2009-01-01

    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 mo...

  9. Strain Gage Measurement System to Determine Cryogenic Propellant Tank Level

    Science.gov (United States)

    Figueroa, Fernando; St.Cyr, William W.; VanDyke, David; McVay, Greg; Mitchell, Mark; Langford, Lester

    2003-01-01

    Measurement of tank level, particularly for cryogenic propellants, has proven to be a difficult proposition. Current methods based on differential pressure, capacitance sensors, temperature sensors, etc.; do not provide sufficiently accurate or robust measurements, especially at run time. This paper describes a simple, but effective method to determine propellant volume by measuring very small deformations of the structure supporting the tank. Results of a laboratory study to validate the method, and experimental data from a deployed system are presented. A comparison with an existing differential pressure sensor shows that the strain gage system provides a very good quality signal even during pressurization.

  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. Automated system for determining the burnup of spent nuclear fuel

    Directory of Open Access Journals (Sweden)

    Mokritskii V. A.

    2014-12-01

    Full Text Available The authors analyze their experience in application of semi-conductor detectors and development of a breadboard model of the monitoring system for spent nuclear fuel (SNF. Such system should use CdZnTe-detectors in which one-charging gathering conditions are realized. The proposed technique of real time SNF control during reloading technological operations is based on the obtained research results. Methods for determining the burnup of spent nuclear fuel based on measuring the characteristics of intrinsic radiation are covered in many papers, but those metods do not usually take into account that the nuclear fuel used during the operation has varying degrees of initial enrichment, or a new kind of fuel may be used. Besides, the known methods often do not fit well into the existing technology of fuel loading operations and are not suitable for operational control. Nuclear fuel monitoring (including burnup determination system in this research is based on the measurement of the spectrum of natural gamma-radiation of irradiated fuel assemblies (IFA, as from the point of view of minimizing the time spent, the measurement of IFA gamma spectra directly during fuel loading is optimal. It is the overload time that is regulated rather strictly, and burnup control operations should be coordinated with the schedule of the fuel loading. Therefore, the real time working capacity of the system should be chosen as the basic criterion when constructing the structure of such burnup control systems.

  12. Star tracker based attitude determination system for nanosatellites

    OpenAIRE

    Jané Abad, Jaume

    2015-01-01

    The aim of this project is to conceive, design, implement, test, qualify, operate, and validate a new high accuracy sensor based on a star sensor for the ADCS subsystem of the 3Cat-2 Mission. This system will implement the necessary algorithms for the star identification and attitude determination in a highly constrained in time, size, mass and power embedded environment. Test and qualification campaign shall be done both in controlled environment and field test. [ANGLÈS] Access to space i...

  13. 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.

  14. Uncertainty determination demonstration program on MC and A measurement systems

    International Nuclear Information System (INIS)

    Statistically propagated limits of error (LOE) for accountability measurements are usually smaller than LOEs derived from historical data. Laboratory measurement quality control programs generate estimates of random and systematic errors for the LOE calculations. The uncertainty of measurement system standards and instrument calibrations are often not included in measurement quality control (QC) programs (MCPs) estimates. Therefore, the uncertainty associated with a measurement system is usually underestimated. A program was conducted at the Savannah River Site (SRS) to evaluate a commercial measurement assurance program software package (JTIPMAP trademark) that records, charts, and analyzes control standard measurements to determine and control total measurement uncertainty. The software uniquely uses the uncertainty of the standards, the calibration histories and routine QC data to estimate the total uncertainty of a measurement process. The demonstration program involved: training measurement personnel on the principles of process measurement assurance (PMAP) and the use of the software; technical support in setting up PMAPs on gas mass spectrometry, calorimetry, Fourier transformed infrared (FTIR) spectrometry, alpha PHA spectrometry, diode array spectrophotometry, and mass standards calibrations measurement systems; and determining and evaluating uncertainty estimates for each system. Results of the demonstration program are described and the uncertainties for these measurement systems are summarized in the paper below. The demonstration showed the training and software provided several useful functions such as uncertainty determinations that include the standards used and independent standards that reveal measurement process systematic errors, which produced larger uncertainties estimates than current MCPs. The software will be tested further in pilot programs for D2O measurements, calorimetry and mass standards calibrations

  15. Determination of cost effective waste management system receipt rates

    International Nuclear Information System (INIS)

    A comprehensive logistics and cost analysis has been carried out to determine if there are potential benefits to the high-level waste management system for receipt rates other than the current 3000 MTU/yr design-basis. The analysis includes both a Repository-Only System and a Storage-Only System. Repository startup dates of 2010 and 2015 and MRS startup dates of 1988 and three years prior to the repository have been evaluated. Receipt rates ranging from 1,500 to 6, 000 MTU/yr have been considered. Higher receipt rates appear to be economically justified, for either system, minimum costs are found at a repository receipt rate of 6000 MTU/yr. However, the MRS receipt rate for minimum system costs depends on the MRS startup date. With a 1988 MRS and a 2010 repository, the added cost of providing the MRS is offset by at-reactor storage cost reductions and the total system cost of $10.0 billion is virtually the same as for the repository- only system. 9 refs., 8 figs., 3 tabs

  16. Study of an alternative system for manganese bath efficiency determination

    International Nuclear Information System (INIS)

    An alternative irradiation system, using radioisotope neutron sources and a small MnSO4 solution volume, was proposed m this work to determine the Manganese Bath System (MBS) efficiency. The irradiation system was characterized through simulations with the MCNP radiation transport code from the modeling of 252Cf(f,n) and 238PuBe(alpha,n) neutron sources in several MnSO4 solution volumes and different neutron reflector medium for this solution. The parameter calculated in the simulations was the manganese neutron specific capture (MNSC), which is related to the MnSO4 solution specific activity. From the proposed systems for 252Cf (f, n) and 238PuBe (alpha,n) the NSCM was increased hundred times, in relation with that achieved in the LN/LNMRI/IRD MBS system simulation when irradiated by each these neutron sources. During study for irradiation system characterization its concept was verified using a assemble of test irradiation (ATI), which were spherical glass cavities, with few centimeter in radius, filled with MnSO4 solution, with and without presence of a neutron reflector medium. These TIA were used in four efficiency measurements and the average value was obtained. (author)

  17. Determination of parameters for digital meter of doppler radars systems for the artillery systems

    OpenAIRE

    Kaninskiy, Valeriy; Budaretskiy, Yuriy; Grabchak, Volodymyr; Prokopenko, Vyacheslav

    2010-01-01

    analytical choice of the digital meter parameters based on digital systems of phase synchronization (DSPS) is considered, also the simulation model design in order to perform the optimization of its parameters and to determine the temporary characteristics and the accuracy of the motion parameters of objects estimating, for the systems with autonomous navigation and ballistic training artillery systems.

  18. 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.

  19. 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.

  20. Parallel Plate System for Collecting Data Used to Determine Viscosity

    Science.gov (United States)

    Kaukler, William (Inventor); Ethridge, Edwin C. (Inventor)

    2013-01-01

    A parallel-plate system collects data used to determine viscosity. A first plate is coupled to a translator so that the first plate can be moved along a first direction. A second plate has a pendulum device coupled thereto such that the second plate is suspended above and parallel to the first plate. The pendulum device constrains movement of the second plate to a second direction that is aligned with the first direction and is substantially parallel thereto. A force measuring device is coupled to the second plate for measuring force along the second direction caused by movement of the second plate.

  1. Attitude Determination System for a Phased Array Beamformer

    OpenAIRE

    Garrucho Moras, Lidia

    2015-01-01

    The project aims to design and build a control system for a new GNSS reflectometer. The instrument has two antenna arrays and it is needed to electronically steer the beams of these arrays (each array has two frequency bands and two beams per band) to point some satellites and the ground point where the transmitted signals from these satellites reflect. To achieve this, the instrument needs to determine the position and attitude of the sensor using GNSS receivers and IMUs and then it will cal...

  2. Storage Size Determination for Grid-Connected Photovoltaic Systems

    OpenAIRE

    Ru, Yu; Kleissl, Jan; 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. Due to the time-of-use electricity pricing, electricity can...

  3. System analysis of the extrusion process to determine the objectives and structure of the control system

    OpenAIRE

    Ярощук, Людмила Дем’янівна; Жученко, Олексій Анатолійович

    2013-01-01

    The article is devoted to the system analysis of the extrusion of polymeric materials in order to determine the objectives and structure of a control system. The algorithm of the system analysis of technological objects of different complexity was suggested on the example of the extrusion process.The algorithm provides the definition of the tasks that are formulated for the production system as a whole: productivity and product quality, economic effectiveness, social and environmental tasks.A...

  4. Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

    Science.gov (United States)

    Yu, Wenbo; He, Xibing; Vanommeslaeghe, Kenno; MacKerell, Alexander D

    2012-12-01

    Presented is an extension of the CHARMM General Force Field (CGenFF) to enable the modeling of sulfonyl-containing compounds. Model compounds containing chemical moieties such as sulfone, sulfonamide, sulfonate, and sulfamate were used as the basis for the parameter optimization. Targeting high-level quantum mechanical and experimental crystal data, the new parameters were optimized in a hierarchical fashion designed to maintain compatibility with the remainder of the CHARMM additive force field. The optimized parameters satisfactorily reproduced equilibrium geometries, vibrational frequencies, interactions with water, gas phase dipole moments, and dihedral potential energy scans. Validation involved both crystalline and liquid phase calculations showing the newly developed parameters to satisfactorily reproduce experimental unit cell geometries, crystal intramolecular geometries, and pure solvent densities. The force field was subsequently applied to study conformational preference of a sulfonamide based peptide system. Good agreement with experimental IR/NMR data further validated the newly developed CGenFF parameters as a tool to investigate the dynamic behavior of sulfonyl groups in a biological environment. CGenFF now covers sulfonyl group containing moieties allowing for modeling and simulation of sulfonyl-containing compounds in the context of biomolecular systems including compounds of medicinal interest. PMID:22821581

  5. 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.

  6. 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.

  7. 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

  8. 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

    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.

  9. On the Role of London Dispersion Forces in Biomolecular Structure Determination

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Kubař, T.; Hobza, Pavel

    2011-01-01

    Roč. 115, č. 24 (2011), s. 8038-8046. ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GAP208/11/0295 Grant ostatní: Korea Science and Ingineering Foundation(KR) R32-2008-000-10180-0; European Scince Found(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : dispersion interaction * DNA * molecular dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.696, year: 2011

  10. Facing and Overcoming Sensitivity Challenges in Biomolecular NMR Spectroscopy

    DEFF Research Database (Denmark)

    Ardenkjær-Larsen, Jan Henrik; Boebinger, Gregory S.; Comment, Arnaud;

    2015-01-01

    of the primary approaches that were considered. Topics discussed included the future of ultrahigh‐field NMR systems, emerging NMR detection technologies, new approaches to nuclear hyperpolarization, and progress in sample preparation. All of these are orthogonal efforts, whose gains could multiply...... optical measurements. These challenges, and the ways by which scientists and engineers are striving to solve them, are also addressed....

  11. Biomolecular Modeling in a Process Dynamics and Control Course

    Science.gov (United States)

    Gray, Jeffrey J.

    2006-01-01

    I present modifications to the traditional course entitled, "Process dynamics and control," which I renamed "Modeling, dynamics, and control of chemical and biological processes." Additions include the central dogma of biology, pharmacokinetic systems, population balances, control of gene transcription, and large­-scale…

  12. Quantum dynamics of complex molecular systems

    OpenAIRE

    Miller, William H.

    2005-01-01

    This Perspective presents a broad overview of the present status of theoretical capabilities for describing quantum dynamics in molecular systems with many degrees of freedom, e.g., chemical reactions in solution, clusters, solids, or biomolecular environments.

  13. 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.

  14. Biomolecular transitions: efficient computation of pathways, free energies, and rates

    CERN Document Server

    Bhatt, Divesh

    2011-01-01

    We present an efficient method to compute transition rates between states for a two-state system. The method utilizes the equivalence between steady-state flux and mean first passage rate for such systems. More specifically, the procedure divides the configurational space into smaller regions and equilibrates trajectories within each region efficiently. The equilibrated conditional probabilities between each pair of regions lead to transition rates between the two states. We apply the procedure to a non-trivial coarse-grained model of a 70 residue section of the calcium binding protein, calmodulin. The procedure yields a significant increase in efficiency compared to brute-force simulations, and this efficiency increases dramatically with a decrease in temperature.

  15. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    OpenAIRE

    Vergara-Perez, Sandra; Marucho, Marcelo

    2015-01-01

    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, de...

  16. Perspectives for quantum interference with biomolecules and biomolecular clusters

    Science.gov (United States)

    Geyer, P.; Sezer, U.; Rodewald, J.; Mairhofer, L.; Dörre, N.; Haslinger, P.; Eibenberger, S.; Brand, C.; Arndt, M.

    2016-06-01

    Modern quantum optics encompasses a wide field of phenomena that are either related to the discrete quantum nature of light, the quantum wave nature of matter or light–matter interactions. We here discuss new perspectives for quantum optics with biological nanoparticles. We focus in particular on the prospects of matter-wave interferometry with amino acids, nucleotides, polypeptides or DNA strands. We motivate the challenge of preparing these objects in a ‘biomimetic’ environment and argue that hydrated molecular beam sources are promising tools for quantum-assisted metrology. The method exploits the high sensitivity of matter-wave interference fringes to dephasing and shifts in the presence of external perturbations to access and determine molecular properties.

  17. 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

  18. Biomolecular crystals for material applications and a mechanistic study of an iron oxide nanoparticle synthesis

    Science.gov (United States)

    Falkner, Joshua Charles

    The three projects within this work address the difficulties of controlling biomolecular crystal formats (i.e. size and shape), producing 3-D ordered composite materials from biomolecular crystal templates, and understanding the mechanism of a practical iron oxide synthesis. The unifying thread consistent throughout these three topics is the development of methods to manipulate nanomaterials using a bottom-up approach. Biomolecular crystals are nanometer to millimeter sized crystals that have well ordered mesoporous solvent channels. The overall physical dimensions of these crystals are highly dependent on crystallization conditions. The controlled growth of micro- and nanoprotein crystals was studied to provide new pathways for creating smaller crystalline protein materials. This method produced tetragonal hen egg-white lysozyme crystals (250--100,000 nm) with near monodisperse size distributions (membranes or templates. In this work, the porous structure of larger cowpea mosaic virus crystals was used to template metal nanoparticle growth within the body centered cubic crystalline network. The final composite material was found to have long range ordering of palladium and platinum nonocrystal aggregates (10nm) with symmetry consistent to the virus template. Nanoparticle synthesis itself is an immense field of study with an array of diverse applications. The final piece of this work investigates the mechanism behind a previously developed iron oxide synthesis to gain more understanding and direction to future synthesis strategies. The particle growth mechanism was found to proceed by the formation of a solvated iron(III)oleate complex followed by a reduction of iron (III) to iron (II). This unstable iron(II) nucleates to form a wustite (FeO) core which serves as an epitaxial surface for the magnetite (Fe3O4) shell growth. This method produces spherical particles (6-60nm) with relative size distributions of less than 15%.

  19. Dynamics of biomoleculars studied by Rayleigh scattering of Moessbauer radiation and Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    This paper reports on dynamics of biomoleculars, proteins and DNA that plays a role in the supply and the regulation their functional activity, for example, like transducers of oxygen, like enzymes, in photosynthesis and so on. The Mossbauer spectroscopy (MS) and especially Rayleigh Scattering of Mossbauer Radiation (RSMR) permit to obtain the quantitative data on dimensions and times of complex hierarchy of motion in biopolymers and to create correspondent functional models. The scheme of RSMR includes Mossbauer source 57Co, the scatterer---biopolymer, the detector and Mossbauer analyzer (Black absorber---or one-line absorber), that situated before and after the scatterer on definite angle -2θ

  20. Surface-plasmon-enhanced fluorescence from periodic quantum dot arrays through distance control using biomolecular linkers

    International Nuclear Information System (INIS)

    We have developed a protein-enabled strategy to fabricate quantum dot (QD) nanoarrays where up to a 15-fold increase in surface-plasmon-enhanced fluorescence has been achieved. This approach permits a comprehensive control both laterally (via lithographically defined gold nanoarrays) and vertically (via the QD-metal distance) of the collectively behaving assemblies of QDs and gold nanoarrays by way of biomolecular recognition. Specifically, we demonstrated the spectral tuning of plasmon resonant metal nanoarrays and self-assembly of protein-functionalized QDs in a stepwise fashion with a concomitant incremental increase in separation from the metal surface through biotin-streptavidin spacer units.

  1. System to determine present elements in oily samples

    International Nuclear Information System (INIS)

    In the Chemistry Department of the National Institute of Nuclear Investigations of Mexico, dedicated to analyze samples of oleaginous material and of another origin, to determine the elements of the periodic table present in the samples, through the Neutron activation analysis technique (NAA). This technique has been developed to determine majority elements in any solid, aqueous, industrial and environmental sample, which consists basically on to irradiate a sample with neutrons coming from the TRIGA Mark III reactor and to carry out the analysis to obtain those gamma spectra that it emits, for finally to process the information, the quantification of the analysis it is carried out in a manual way, which requires to carry out a great quantity of calculations. The main objective of this project is the development of a software that allows to carry out the quantitative analysis of the NAA for the multielemental determination of samples in an automatic way. To fulfill the objective of this project it has been divided in four chapters: In the first chapter it is shortly presented the history on radioactivity and basic concepts that will allow us penetrate better to this work. In the second chapter the NAA is explained which is used in the sample analysis, the description of the process to be carried out, its are mentioned the characteristics of the used devices and an example of the process is illustrated. In the third chapter it is described the development of the algorithm and the selection of the programming language. The fourth chapter it is shown the structure of the system, the general form of operation, the execution of processes and the obtention of results. Later on the launched results are presented in the development of the present project. (Author)

  2. 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.

  3. 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...

  4. 78 FR 68432 - Applicability Determination Index (ADI) Database System Recent Posting: Applicability...

    Science.gov (United States)

    2013-11-14

    ... AGENCY Applicability Determination Index (ADI) Database System Recent Posting: Applicability... the Applicability Determination Index (ADI) database system is available on the Internet through the... for each document posted on the ADI database system on October 30, 2013; the applicable category;...

  5. Double-gated spectral snapshots for biomolecular fluorescence

    International Nuclear Information System (INIS)

    A versatile method to take femtosecond spectral snapshots of fluorescence has been developed based on a double gating technique in the combination of an optical Kerr gate and an image intensifier as an electrically driven gate set in front of a charge-coupled device detector. The application of a conventional optical-Kerr-gate method is limited to molecules with the short fluorescence lifetime up to a few hundred picoseconds, because long-lifetime fluorescence itself behaves as a source of the background signal due to insufficiency of the extinction ratio of polarizers employed for the Kerr gate. By using the image intensifier with the gate time of 200 ps, we have successfully suppressed the background signal and overcome the application limit of optical-Kerr-gate method. The system performance has been demonstrated by measuring time-resolved fluorescence spectra for laser dye solution and the riboflavin solution as a typical sample of biomolecule

  6. Criteria for Determination of Material Control and Accountability System Effectiveness

    International Nuclear Information System (INIS)

    The Nevada Test Site (NTS) is a test bed for implementation of the Safeguards First Principles Initiative (SFPI), a risk-based approach to Material Control and Accountability (MC and A) requirements. The Comprehensive Assessment of Safeguards Strategies (COMPASS) model is used to determine the effectiveness of MC and A systems under SFPI. Under this model, MC and A is divided into nine primary elements. Each element is divided into sub-elements. Then each sub-element is assigned two values, effectiveness and contribution, that are used to calculate the rating. Effectiveness is a measure of subelement implementation and how well it meets requirements. Contribution is a relative measure of the importance, and functions as a weighting factor. The COMPASS model provides the methodology for calculation of sub-element and element ratings, but not the actual criteria. Each site must develop its own criteria. For the rating to be meaningful, the effectiveness criteria must be objective and based on explicit, measurable criteria. Contribution (weights) must reflect the importance within the MC and A program. This paper details the NTS approach to system effectiveness and contribution values, and will cover the following: the basis for the ratings, an explanation of the contribution 'weights', and the objective, performance based effectiveness criteria. Finally, the evaluation process will be described

  7. Criteria for Determination of MC and A System Effectiveness

    International Nuclear Information System (INIS)

    The Nevada Test Site (NTS) is a test bed for implementation of the Safeguards First Principles Initiative (SFPI), a risk-based approach to Material Control and Accountability (MC and A) requirements. The Comprehensive Assessment of Safeguards Strategies (COMPASS) model is used to determine the effectiveness of safeguards systems under SFPI. Under this model, MC and A is divided into nine primary elements. Each element is divided into sub-elements. Then, each sub-element is assigned two values, effectiveness and contribution, that are used to calculate the rating. Effectiveness is a measure of sub-element implementation and how well it meets requirements. Contribution is a relative measure of the importance, and functions as a weighting factor. The COMPASS model provides the methodology for calculation of element and subelement, but not the actual criteria. Each site must develop its own criteria. For the rating to be meaningful, the effectiveness criteria must be objective and based on explicit, measurable criteria. Contribution (weights) must reflect the importance within the MC and A program. This paper details the NTS approach to system effectiveness and contribution values, and will cover the following: the basis for the ratings, an explanation of the contribution weights, and the objective, performance-based effectiveness criteria. Finally, the evaluation process will be described

  8. Hybrid expert system implementation to determine core reload patterns

    International Nuclear Information System (INIS)

    Determining reactor reload fuel patterns is a computationally intensive problem solving process for which automation can be of significant benefit. Often much effort is expended in the search for an optimal loading. While any modern programming language could be used to automate solution, the specialized tools of artificial intelligence (AI) are the most efficient means of introducing the fuel management expert's knowledge into the search for an optimum reload pattern. Prior research in pressurized water reactor refueling strategies developed FORTRAN programs that automated an expert's basic knowledge to direct a search for an acceptable minimum peak power loading. The dissatisfaction with maintenance of compiled knowledge in FORTRAN programs has served as the motivation for the development of the SHUFFLE expert system. SHUFFLE is written in Smalltalk, an object-oriented programming language, and evaluates loadings as it generates them using a two-group, two-dimensional nodal power calculation compiled in a personal computer-based FORTRAN. This paper reviews the object-oriented representation developed to solve the core reload problem with an expert system tool and its operating prototype, SHUFFLE

  9. Biomolecular pleiomorphism probed by spatial interpolation of coarse models.

    Science.gov (United States)

    Rusu, Mirabela; Birmanns, Stefan; Wriggers, Willy

    2008-11-01

    In low resolution structures of biological assemblies one can often observe conformational deviations that require a flexible rearrangement of structural domains fitted at the atomic level. We are evaluating interpolation methods for the flexible alignment of atomic models based on coarse models. Spatial interpolation is well established in image-processing and visualization to describe the overall deformation or warping of an object or an image. Combined with a coarse representation of the biological system by feature vectors, such methods can provide a flexible approximation of the molecular structure. We have compared three well-known interpolation techniques and evaluated the results by comparing them with constrained molecular dynamics. One method, inverse distance weighting interpolation, consistently produced models that were nearly indistinguishable on the alpha carbon level from the molecular dynamics results. The method is simple to apply and enables flexing of structures by non-expert modelers. This is useful for the basic interpretation of volumetric data in biological applications such as electron microscopy. The method can be used as a general interpretation tool for sparsely sampled motions derived from coarse models. PMID:18757874

  10. Microfluidic multiculture assay to analyze biomolecular signaling in angiogenesis.

    Science.gov (United States)

    Theberge, Ashleigh B; Yu, Jiaquan; Young, Edmond W K; Ricke, William A; Bushman, Wade; Beebe, David J

    2015-03-17

    Angiogenesis (the formation of blood vessels from existing blood vessels) plays a critical role in many diseases such as cancer, benign tumors, and macular degeneration. There is a need for cell culture methods capable of dissecting the intricate regulation of angiogenesis within the microenvironment of the vasculature. We have developed a microscale cell-based assay that responds to complex pro- and antiangiogenic soluble factors with an in vitro readout for vessel formation. The power of this system over traditional techniques is that we can incorporate the whole milieu of soluble factors produced by cells in situ into one biological readout (vessel formation), even if the identity of the factors is unknown. We have currently incorporated macrophages, endothelial cells, and fibroblasts into the assay, with the potential to include additional cell types in the future. Importantly, the microfluidic platform is simple to operate and multiplex to test drugs targeting angiogenesis in a more physiologically relevant context. As a proof of concept, we tested the effect of an enzyme inhibitor (targeting matrix metalloproteinase 12) on vessel formation; the triculture microfluidic assay enabled us to capture a dose-dependent effect entirely missed in a simplified coculture assay (p < 0.0001). This result underscores the importance of cell-based assays that capture chemical cross-talk occurring between cell types. The microscale dimensions significantly reduce cell consumption compared to conventional well plate platforms, enabling the use of limited primary cells from patients in future investigations and offering the potential to screen therapeutic approaches for individual patients in vitro. PMID:25719435

  11. Spatially encoded strategies in the execution of biomolecular-oriented 3D NMR experiments

    International Nuclear Information System (INIS)

    Three-dimensional nuclear magnetic resonance (3D NMR) provides one of the foremost analytical tools available for the elucidation of biomolecular structure, function and dynamics. Executing a 3D NMR experiment generally involves scanning a series of time-domain signals S(t3), as a function of two time variables (t1, t2) which need to undergo parametric incrementations throughout independent experiments. Recent years have witnessed extensive efforts towards the acceleration of this kind of experiments. Among the different approaches that have been proposed counts an 'ultrafast' scheme, which distinguishes itself from other propositions by enabling-at least in principle-the acquisition of the complete multidimensional NMR data set within a single transient. 2D protein NMR implementations of this single-scan method have been demonstrated, yet its potential for 3D acquisitions has only been exemplified on model organic compounds. This publication discusses a number of strategies that could make these spatial encoding protocols compatible with 3D biomolecular NMR applications. These include a merging of 2D ultrafast NMR principles with temporal 2D encoding schemes, which can yield 3D HNCO spectra from peptides and proteins within ∼100 s timescales. New processing issues that facilitate the collection of 3D NMR spectra by relying fully on spatial encoding principles are also assessed, and shown capable of delivering HNCO spectra within 1 s timescales. Limitations and prospects of these various schemes are briefly addressed

  12. 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.

  13. Neutral-particle emission in collisions of electrons with biomolecular ions in an electrostatic storage ring

    International Nuclear Information System (INIS)

    Electron-biomolecular ion collisions were studied using an electrostatic storage ring with a merging electron beam device. Biomolecular ions produced by an electrospray ion source and accelerated to 20 keV/charge were injected into the ring after being mass-analyzed. The circulating ion beam was then merged with an electron beam. Neutral reaction products in collisions of electrons with ions were detected by a micro-channel plate outside of the ring. Electron-ion collisions were studied for multiply-deprotonated oligonucleotide and peptide anions as well as singly protonated oligonucleotide and peptide cations. For peptide cations, neutrals were resonantly emitted at an electron energy of around 6.5 eV, which was almost independent of the ion masses. This is deduced to come from electron-ion recombination, resulting in the cleavage of a peptide bond. For DNA oligonucleotide cations, resonant neutral particle emission was also observed. In electron and DNA anion collisions, neutrals started to increase from definite threshold energies, where the threshold energies increased in proportion to the ion charge. The same was found for peptide anions. The origin of this phenomenon is discussed

  14. X3DBio2: A visual analysis tool for biomolecular structure comparison

    Science.gov (United States)

    Yi, Hong; Thakur, Sidharth; Sethaphong, Latsavongsakda; Yingling, Yaroslava G.

    2013-01-01

    A major problem in structural biology is the recognition of differences and similarities between related three dimensional (3D) biomolecular structures. Investigating these structure relationships is important not only for understanding of functional properties of biologically significant molecules, but also for development of new and improved materials based on naturally-occurring molecules. We developed a new visual analysis tool, X3DBio2, for 3D biomolecular structure comparison and analysis. The tool is designed for elucidation of structural effects of mutations in proteins and nucleic acids and for assessment of time dependent trajectories from molecular dynamics simulations. X3DBio2 is a freely downloadable open source software and provides tightly integrated features to perform many standard analysis and visual exploration tasks. We expect this tool can be applied to solve a variety of biological problems and illustrate the use of the tool on the example study of the differences and similarities between two proteins of the glycosyltransferase family 2 that synthesize polysaccharides oligomers. The size and conformational distances and retained core structural similarity of proteins SpsA to K4CP represent significant epochs in the evolution of inverting glycosyltransferases.

  15. 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. PMID:26410586

  16. Group transfer theory of single molecule imaging experiments in the F-ATPase biomolecular motor

    Science.gov (United States)

    Volkan-Kacso, Sandor; Marcus, Rudolph

    I describe a chemo-mechanical theory to treat single molecule imaging and ``stalling'' experiments on the F-ATPase enzyme. This enzyme is an effective stepping biomolecular rotary motor with a rotor shaft and a stator ring. Using group transfer theoretical approach the proposed structure-based theory couples the binding transition of nucleotides in the stator subunits and the physics of torsional elasticity in the rotor. The twisting of the elastic rotor domain acts as a perturbation upon the driving potential, the Gibbs free energy. In the theory, without the use of adjustastable parameters, we predict the rate and equilibrium constant dependence of steps such as ATP binding and phosphate release as a function of manipulated rotor angle. Then we compare these predictions to available data from stalling experiments. Besides treating experiments, the theory can provide guides for atomistic simulations, which could calculate the reorganization parameter and the torsional spring constant. The framework is generic and I discuss its application to other single molecule experiments, such as controlled rotation and other biomolecular motors, including motor-DNA complexes and linear motors.[PNAS, Early Edition, Oct. 19, 2015, doi: 10.1073/pnas.1518489112

  17. 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. factores ligados a la definición de producción sostenible los cuales no son fácil de cuantificar, (5) frecuentemente existe confusión entre la producción optima de un establecimiento y la producción sostenible de unacuenca, (6) en muchos ambientes áridos a semi-áridos los sistemas de aguas subterráneas no pueden desarrollarse sensiblemente en base a una política de producción sostenible particularmente donde se aplican restricciones ecológicas. La derivación de producción sostenible utilizando principios de conservación de masa conduce a expresiones para producciones sostenibles en cuenca, minado parcial (no

  18. 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...

  19. Using Geo-informational System for determining land degradation processes

    Science.gov (United States)

    Mangul, I.; Mangul, S.

    The largest part of agricultural lands of the Republic of Moldova is concentrated in the arid zone Frequent droughts once in 2-4 years inflict vital causalities to agriculture of the Republic of Moldova However droughts influence doesn t only limit itself to forming production Drought after-effect is highly ruinous for water reserves industrial enterprises functioning rhythm and human health Droughts make for the drying up and crumbling of soil which is subject to excessive human influence and result in land degradation desertification Term desertification means land degradation in the droughty zones It is necessary to mention that the droughty ecosystems are extremely fragile and sensitive overexploitation Nowadays in the Republic of Moldova 33-37 of agricultural lands is eroded Republic of Moldova joined the United Nations Convention to Combat Desertification on December 24 1998 The Government of the Republic of Moldova ratified the National Action Plan to Combat Desertification in 2000 Within the framework of executing the National Action Plan by National Committee to Combat Desertification Geo-informational System on arid questions was organized In addition a lot of indexes corresponding to international standards were used for the evaluation of drought of the territory and land degradation processes Mostly this information is presented in maps erosion landslides aridity water resources A rich experience of using satellite information for determining land degradation demonstrates high effectiveness of this method Satellite

  20. Determination of Fracture System Geometry from Well Testing

    International Nuclear Information System (INIS)

    In this paper, the research and development for the description of the hydraulic geometry of fracture networks are discussed. The studies on fracture networks have developed on the premise that the structural geological information on fracture geometries could be used to develop the realistic models of flow. It has been widely recognized that a relatively small portion of natural fracture networks controls a major portion of groundwater flow. The key to efficient network modeling is to identify that portion of networks. It is the main purpose of this paper to discuss the methods for characterizing the hydraulic geometry of fracture flow systems. The methods described in this paper cover three approaches for defining the hydraulic geometry of fracture networks, that is, the determination of conductive fracture frequency in boreholes, the use of transient pressure and flow responses in single holes, and the use of cross hole test to assess connectivity. The information which can be obtained by each test is shown. Flow logging, well test distribution and conductive fracture frequency are discussed. The transient analysis of single hole well test and the cross hole analysis of well test for fracture network geometry are reported. The data taken by various methods together can provide network characterization. (K.I.)

  1. Influence of affinity on antibody determination in microtiter ELISA systems

    International Nuclear Information System (INIS)

    Theoretically, all immunoassays are affinity (Ka) dependent when the product of the antibody (Ab) Ka and the free epitope concentration is less than 10. Thus, the degree of dependence on Ka depends on the concentration of available antigen in the system. The authors examined the binding of 125I-anti-fluorescein (a-FLU) monoclonal antibodies of different affinities to FLU-gelatin adsorbed on Immunlon 2 microtiter plates. Data obtained were in general agreement with our theoretical predictions; the percent of 125I-a-FLU which bound correlated with Ka, as did the shape of the titration curves. Measurement of 5 a-FLU monoclonals by the ELISA showed that the determination of Ab concentrations depends on the FLU-gelatin concentration, epitope density, and on the relationship between the Kas of test samples and the reference standard Ab preparation. Thus the ELISA is Ka dependent and should not be used routinely to estimate the absolute amount to Ab in unknown samples. However, the Ka dependency of the ELISA might provide a convenient assay for the estimation of the relative functional Ka (rfKa) of antibody preparations

  2. Methodology for determining the value of wind energy conversion systems for specific utility systems

    Science.gov (United States)

    1981-09-01

    The methodology uses to the maximum extent possible techniques that the electric utility industry developed to determine the relative economic attractiveness of alternative generation expansion plans. Three factors are emphasized in the methodology: the site dependence of wind resources, the inability to control the electrical output of wind energy conversion systems, and the lack of reliable WECS cost information.

  3. 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....... applied 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....

  4. Biomolecular motors

    Directory of Open Access Journals (Sweden)

    Henry Hess

    2005-12-01

    Here, we give a brief introduction to molecular motors, with an emphasis on motor proteins, describe the challenges in interfacing these bionanomachines with an artificial environment, and provide examples of emerging applications.

  5. Small-angle X-ray scattering investigations of biomolecular confinement, loading, and release from liquid-crystalline nanochannel assemblies

    Czech Academy of Sciences Publication Activity Database

    Angelova, A.; Angelov, Borislav; Garamus, V. M.; Couvreur, P.; Lesieur, S.

    2012-01-01

    Roč. 3, č. 3 (2012), s. 445-457. ISSN 1948-7185 Institutional research plan: CEZ:AV0Z40500505 Keywords : nanochannels * biomolecular nanostructures * SAXS Subject RIV: CD - Macromolecular Chemistry Impact factor: 6.585, year: 2012

  6. 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…

  7. 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.

  8. Sex-determination systems and their evolution: Mammals

    International Nuclear Information System (INIS)

    Sex-determination methods are very diverse as they have become an enduring research field, understanding the causes of gonadal development and elucidating the main factors involved in sex-determination of offspring required relating information from far-ranging areas such as cytology, embryology, morphology, molecular biology and even ecology and evolution. This article presents an overview of sex-determination in placental mammals, encompassing several levels of biological organization. The importance of the underlying molecular tools in the context of sex-determination assays and their implications in conservation genetics is also discussed.

  9. Determinants of Banking System Fragility : A Regional Perspective

    OpenAIRE

    Degryse, H.A.; Elahi, M.A.; Penas, M.F.

    2012-01-01

    Abstract: Banking systems are fragile not only within one country but also within and across regions. We study the role of regional banking system characteristics for regional banking system fragility. We find that regional banking system fragility reduces when banks in the region jointly hold more liquid assets, are better capitalized, and when regional banking systems are more competitive. For Asia and Latin-America, a greater presence of foreign banks also reduces regional banking fragilit...

  10. 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

  11. 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......),enzyme-linkedimmunosorbentassay(EIA),andenzyme linkedlectinassay(ELLA).Theconformationand hydrodynamic diameter of highly purified BSM molecules, as characterized by circular dichroism (CD) spectroscopy and dynamic light scattering (DLS), respectively, showed a slight, yet gradual coiling and compaction in response to the increase in BSM concentration in bulk...

  12. Biomolecular ion detection using high-temperature superconducting MgB2 strips

    Science.gov (United States)

    Zen, N.; Shibata, H.; Mawatari, Y.; Koike, M.; Ohkubo, M.

    2015-06-01

    Superconducting strip ion detectors (SSIDs) are promising for realization of ideal ion detection with 100% efficiency and nanosecond-scale time response in time-of-flight mass spectrometry. We have detected single biomolecular ions in the keV range using a 10-nm-thick and 250-nm-wide strip of a high temperature superconductor, magnesium diboride (MgB2), at temperatures of up to 13 K. The output pulse shape is explained remarkably well using circuit simulations and time-dependent Ginzburg-Landau simulations coupled with a heat diffusion equation. The simulations show that the hot spot model is applicable to the proposed MgB2-SSIDs and the normal region expansion is completed within 16 ps, which corresponds to a maximum length of 1010 nm.

  13. 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.

  14. Method for determining the power loss in the contact system

    Directory of Open Access Journals (Sweden)

    T.I. Kiriluk

    2012-12-01

    Full Text Available The authors offer conferencing method for determining the power loss coefficient for the contact network. Authors have received expressions for the equivalent value of loss coefficient for the existing power schemes contact network.

  15. Price Determination and Stabilization Under Free Banking System

    OpenAIRE

    Süleyman DEĞİRMEN

    2000-01-01

    In the past the long run objective of monetary policy was a balanced budget, but more recently it has focussed on price stability. Price level stabilization had many proponents during the 1920s and 1930s and continues to have advocates today. The central banks of the US, New Zealand, Germany, and others espoused it during the last two decades. Price level determination and hence stabilization are important issues for economies since they determine the expectations of policy makers and individ...

  16. Biomolecular Characterization of Diazotrophs Isolated from the Tropical Soil in Malaysia

    Directory of Open Access Journals (Sweden)

    Zulkifli H Shamsuddin

    2013-08-01

    Full Text Available This study was conducted to evaluate selected biomolecular characteristics of rice root-associated diazotrophs isolated from the Tanjong Karang rice irrigation project area of Malaysia. Soil and rice plant samples were collected from seven soil series belonging to order Inceptisol (USDA soil taxonomy. A total of 38 diazotrophs were isolated using a nitrogen-free medium. The biochemical properties of the isolated bacteria, such as nitrogenase activity, indoleacetic acid (IAA production and sugar utilization, were measured. According to a cluster analysis of Jaccard’s similarity coefficients, the genetic similarities among the isolated diazotrophs ranged from 10% to 100%. A dendogram constructed using the unweighted pair-group method with arithmetic mean (UPGMA showed that the isolated diazotrophs clustered into 12 groups. The genomic DNA rep-PCR data were subjected to a principal component analysis, and the first four principal components (PC accounted for 52.46% of the total variation among the 38 diazotrophs. The 10 diazotrophs that tested highly positive in the acetylene reduction assay (ARA were identified as Bacillus spp. (9 diazotrophs and Burkholderia sp. (Sb16 using the partial 16S rRNA gene sequence analysis. In the analysis of the biochemical characteristics, three principal components were accounted for approximately 85% of the total variation among the identified diazotrophs. The examination of root colonization using scanning electron microscopy (SEM and transmission electron microscopy (TEM proved that two of the isolated diazotrophs (Sb16 and Sb26 were able to colonize the surface and interior of rice roots and fixed 22%–24% of the total tissue nitrogen from the atmosphere. In general, the tropical soils (Inceptisols of the Tanjong Karang rice irrigation project area in Malaysia harbor a diverse group of diazotrophs that exhibit a large variation of biomolecular characteristics.

  17. 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

  18. Graph-theoretical identification of dissociation pathways on free energy landscapes of biomolecular interaction.

    Science.gov (United States)

    Wang, Ling; Stumm, Boris; Helms, Volkhard

    2010-03-01

    Biomolecular association and dissociation reactions take place on complicated interaction free energy landscapes that are still very hard to characterize computationally. For large enough distances, though, it often suffices to consider the six relative translational and rotational degrees of freedom of the two particles treated as rigid bodies. Here, we computed the six-dimensional free energy surface of a dimer of water-soluble alpha-helices by scanning these six degrees of freedom in about one million grid points. In each point, the relative free energy difference was computed as the sum of the polar and nonpolar solvation free energies of the helix dimer and of the intermolecular coulombic interaction energy. The Dijkstra graph algorithm was then applied to search for the lowest cost dissociation pathways based on a weighted, directed graph, where the vertices represent the grid points, the edges connect the grid points and their neighbors, and the weights are the reaction costs between adjacent pairs of grid points. As an example, the configuration of the bound state was chosen as the source node, and the eight corners of the translational cube were chosen as the destination nodes. With the strong electrostatic interaction of the two helices giving rise to a clearly funnel-shaped energy landscape, the eight lowest-energy cost pathways coming from different orientations converge into a well-defined pathway for association. We believe that the methodology presented here will prove useful for identifying low-energy association and dissociation pathways in future studies of complicated free energy landscapes for biomolecular interaction. PMID:19603501

  19. The Financial System in China: Determinants and Future

    OpenAIRE

    Teng, Xiaowen

    2007-01-01

    The surprising growth rate of China's economy has been put important attention by the rest of the world. However, whether China's economy could keep on developing at such rate is pending. Since one country's economy cannot grow healthily and rapidly without the support of an appropriate financial system, it is very important to analyze the factors that affect China's financial system for the further development of its financial system, and thereby its economy. This paper primarily uses s...

  20. System and method to determine electric motor efficiency using an equivalent circuit

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Bin; Habetler, Thomas G.

    2015-10-27

    A system and method for determining electric motor efficiency includes a monitoring system having a processor programmed to determine efficiency of an electric motor under load while the electric motor is online. The determination of motor efficiency is independent of a rotor speed measurement. Further, the efficiency is based on a determination of stator winding resistance, an input voltage, and an input current. The determination of the stator winding resistance occurs while the electric motor under load is online.

  1. 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...

  2. Test system accurately determines tensile properties of irradiated metals at cryogenic temperatures

    Science.gov (United States)

    Levine, P. J.; Skalka, R. J.; Vandergrift, E. F.

    1967-01-01

    Modified testing system determines tensile properties of irradiated brittle-type metals at cryogenic temperatures. The system includes a lightweight cryostat, split-screw grips, a universal joint, and a special temperature control system.

  3. 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.

  4. System and technique for ultrasonic determination of degree of cooking

    Science.gov (United States)

    Bond, Leonard J.; Diaz, Aaron A.; Judd, Kayte M.; Pappas, Richard A.; Cliff, William C.; Pfund, David M.; Morgen, Gerald P.

    2007-03-20

    A method and apparatus are described for determining the doneness of food during a cooking process. Ultrasonic signal are passed through the food during cooking. The change in transmission characteristics of the ultrasonic signal during the cooking process is measured to determine the point at which the food has been cooked to the proper level. In one aspect, a heated fluid cooks the food, and the transmission characteristics along a fluid-only ultrasonic path provides a reference for comparison with the transmission characteristics for a food-fluid ultrasonic path.

  5. Computer program determines performance efficiency of remote measuring systems

    Science.gov (United States)

    Merewether, E. K.

    1966-01-01

    Computer programs control and evaluate instrumentation system performance for numerous rocket engine test facilities and prescribe calibration and maintenance techniques to maintain the systems within process specifications. Similar programs can be written for other test equipment in an industry such as the petrochemical industry.

  6. Analytical determination of distillation boundaries for ternary azeotropic systems

    OpenAIRE

    Marcilla Gomis, Antonio; Reyes Labarta, Juan Antonio; Velasco, Raúl; Serrano Cayuelas, María Dolores; Olaya López, María del Mar

    2009-01-01

    A new straight forward algorithm to calculate distillation boundaries in ternary azeotropic systems has been developed. The proposed method allows, using cubic splines, the calculation of distillation trajectories and the calculation of that corresponding to the searched distillation boundaries. The algorithm is applied to 4 ternary liquid-vapour systems to test its validity.

  7. 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…

  8. Determination of BWR stability characteristics from numerically obtained system responses

    International Nuclear Information System (INIS)

    To determine the stability characteristics of a Boiling Water Reactor with reactor safety codes, one usually uses directly the numerically estimated time responses to a square-shaped or triangular-shaped input perturbation. In this way, the determined stability characteristics depend on the perturbation chosen. The stability characteristics would not depend on the perturbation when they are based on the impulse response. Therefore, a rather straightforward method has been used in order to determine the reactor transfer function and the impulse response from the time signals. The calculated response does not depend on the input perturbation shape used when three things are taken into account. First, the amplitude of the perturbation should not be too large in order to avoid the influence of non-linear effects. Second, the frequency content of the input perturbation should be such that the relevant frequency range for the reactor transfer function is covered. Third, the amplitude and width of the perturbations should be such that the perturbation impact is large enough. For a reference case, the transfer function and impulse response have been determined with RELAP5 to demonstrate the method. With this method one uniquely defines the response for which the stability characteristics are to be evaluated. Furthermore, a direct comparison of impulse response or reactor transfer function between calculation and experiment is possible. (author)

  9. Determination of Transmission Limits on Electric Power Systems

    Directory of Open Access Journals (Sweden)

    Castellanos-Bustamante Rafael

    2014-04-01

    Full Text Available This article provides the application of several methodologies to obtain power transmission limits through interties of the electric power systems to obtain a secure operation of the energy power system. Several aspects to obtain the maximum power flows of electrical energy thought of transmission lines on electrical grids are shown. Thermal limit of electrical conductors, loadability limit of transmission lines and small signal stability limits are obtained for several interties between geographical regions. It also, shows the application of a load shedding scheme to stabilize an interarea oscillation mode. The model of the Mexican Interconnected power System is used to illustrate these methodologies.

  10. Determining safe shutdown systems and seismic upgrade priorities

    International Nuclear Information System (INIS)

    This paper describes how lessons learned from US and Western Europe safety improvement programs as well as insights in WWER systems can be used to perform top level seismic safety assessments and narrow the scope of WWER seismic upgrading while still satisfying enhanced safety goals. A clear definition and understanding of the systems requirements and interactions with other possible upgrades is a prerequisite to a practical and effective seismic upgrade program. (author)

  11. Decentralized diagnosis in a spacecraft attitude determination and control system

    OpenAIRE

    Pérez, Carlos Gustavo; Travé-Massuyès, Louise; Chanthery, Elodie; Sotomayor, Javier

    2015-01-01

    In model-based diagnosis (MBD), structural models can provide useful information for fault diagnosis and fault-tolerant control design. In particular, they are known for supporting the design of analytical redundancy relations (ARRs) which are widely used to generate residuals for diagnosis. On the other hand, systems are increasingly complex whereby it is necessary to develop decentralized architectures to perform the diagnosis task. Decentralized diagnosis is of interest for on-board system...

  12. Determinants of Strategic Utilization of Information Systems: A Conceptual Framework

    OpenAIRE

    Mohamad Noorman Masrek; Adnan Jamaludin; Dang Merduwati Hashim

    2009-01-01

    Information technology and information systems have been generally recognized as one of the greatest human inventions of modern times. Information system (IS) is an organized combination of people, hardware, software, communication networks and data resources that collect, transform, and disseminate information in an organization [38]. As IS are being developed and deployed, research on their strategic utilization have been continuously studied by researchers and scholars. Accordingly, variou...

  13. Determination of fractal dimensions from equivalent L systems

    OpenAIRE

    Ortega, Alfonso; Alfonseca, Manuel

    2001-01-01

    This paper revises a few existing methods for computing fractal dimensions, underlines their dependency on the graphical properties of the curves, and proposes and discusses a new method, based on the representation of fractals by means of Lindenmayer systems, that makes use of the structure of L systems to compute the fractal dimension. The method is implemented in Prolog, and its limitations and usefulness are discussed.

  14. 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.

  15. 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.

  16. The determination of planetary structure in tidally relaxed inclined systems

    OpenAIRE

    Mardling, Rosemary A.

    2010-01-01

    [Abridged] The recent discovery of a transiting planet on a non-circular orbit with a massive highly eccentric companion orbiting HAT-P-13 offers the possibility of probing the structure of the short-period planet. The ability to do this relies on the system being in a quasi-equilibrium state in the sense that the eccentricities are constant on the usual secular timescale, and decay on a timescale which is much longer than the age of the system. Since the equilibrium eccentricity is effective...

  17. Determining the impact of a design change on system availability

    International Nuclear Information System (INIS)

    Reliability based approaches together with the use of plant operating experience have an important role in all stages of safety analyses. The assessment and the checking of the nuclear power plant safety is one of the safety principles; its application is intended to lead to the improvement of safety in all the states that have operating nuclear power plants. The applications of probabilistic safety analysis, PSA, studies can be used: -as source for the risk knowledge; - in assessment of plant design; - in accident management -in risk analyses (risk assessment); - in operating applications; - in component maintenance and testing prioritization. The PSA is an efficient system analysis method, which is used to assess the risk of operation of nuclear power plants. The PSA study can be used in order to evaluate the design of a plant, to highlight some design changes, or to evaluate the impact of the design changes implementation. The paper presents a case study regarding the design change of boiler level control station system, by studying the effect of implementation of a design change regarding the motorized valves of the feed water auxiliary circuit. The sensitivity analyses are a part of the probabilistic safety evaluation of the Cernavoda nuclear plant safety. The study presents the sensitivity analysis performed for the following top event: the failure of SG level control station, after loss of BLC or both computers (in case of blackout). The analyzed design change notice (DCN451) consists in the implementation of automatic closure of the auxiliary feedwater motorized valves of the boiler level control stations on a high level signal. Failure criteria appears to be any SG unsupplied, in cooldown, using small flow lines under manual control for a mission time of 24 hours The major function of the BLC system is to maintain the steam generators level as close as it can to the setpoint value, in normal and abnormal operating conditions. The system should operate

  18. 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.

  19. How Does Our Motor System Determine Its Learning Rate?

    OpenAIRE

    Beers, Van, Eduard J.

    2012-01-01

    Motor learning is driven by movement errors. The speed of learning can be quantified by the learning rate, which is the proportion of an error that is corrected for in the planning of the next movement. Previous studies have shown that the learning rate depends on the reliability of the error signal and on the uncertainty of the motor system’s own state. These dependences are in agreement with the predictions of the Kalman filter, which is a state estimator that can be used to determine the o...

  20. 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

  1. 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.

  2. The determinants of the education system in Gazankulu / Wilson Mzamani Ngomani

    OpenAIRE

    Ngomani, Wilson Mzamani

    1989-01-01

    This research study concentrates on exposing the determinants of the education system in Gazankulu. It is universally accepted that there are factors which cause the development of an education system. An education system has both universal and individual factors that make it a unique education system. The problem is "which are these individual factors in Gazankulu which make it a unique education system?" This research aims at revealing these determinants that give shape to the course of dev...

  3. Interaction of growth-determining systems with gravity

    Science.gov (United States)

    Merkys, A.; Laurinavičius, R.; Bendoraityté, D.; Švegždiené, D.; Rupainiené, O.

    The experiments have been carried out with lettuce shoots on board the Salyut-7 orbital station, the Kosmos-1667 biological satellite and under ground conditions at 180° plant inversion. By means of the centrifuge Biogravistat-1M the threshold value of gravitational sensitivity of lettuce shoots has been determined on board the Salyut-7 station. It was found to be equal to 2.9 × 10-3g for hypocotyls and 1.5 × 10-4g for roots. The following results have been received in the experiment performed on board the Kosmos-1667 satellite: a) under microgravity the proliferation of the meristem cells and the growth of roots did not differ from the control; b) the growth of hypocotyls in length was significantly enhanced in microgravity; c) under microgravity transverse growth of hypocotyls (increase in cross sectional area) was significantly increased due to enhancement of cortical parenchyma cell growth. At 180° inversion in Earth's gravity root extension growth and rate of cell division in the root apical meristem were decreased. The determination of DNA-fuchsin value in the nuclei of the cell root apexes showed that inversion affected processess of the cell cycle preceeding cytokinesis.

  4. Interaction of growth-determining systems with gravity.

    Science.gov (United States)

    Merkys, A; Laurinavicius, R; Bendoraityte, D; Svegzdiene, D; Rupainiene, O

    1986-01-01

    The experiments have been carried out with lettuce shoots on board the Salyut-7 orbital station the Kosmos-1667 biological satellite and under ground conditions at 180 degrees plant inversion. By means of the centrifuge Biogravistat-1M the threshold value of gravitational sensitivity of lettuce shoots has been determined on board the Salyut-7 station. It was found to be equal to 2.9 x 10(-3)g for hypocotyls and 1.5 x 10(-4)g for roots. The following results have been received in the experiment performed on board the Kosmos-1667 satellite: a) under microgravity the proliferation of the meristem cells and the growth of roots did not differ from the control; b) the growth of hypocotyls in length was significantly enhanced in microgravity; c) under microgravity transverse growth of hypocotyls (increase in cross sectional area) was significantly increased due to enhancement of cortical parenchyma cell growth. At 180 degrees inversion in Earth's gravity root extension growth and rate of cell division in the root apical meristem were decreased. The determination of DNA-fuchsin value in the nuclei of the cell root apexes showed that inversion affected processes of the cell cycle preceding cytokinesis. PMID:11537846

  5. System for star catalog equalization to enhance attitude determination

    Science.gov (United States)

    Liu, Yong (Inventor); Wu, Yeong-Wei Andy (Inventor); Li, Rongsheng (Inventor)

    2001-01-01

    An apparatus for star catalog equalization to enhance attitude determination includes a star tracker, a star catalog and a controller. The star tracker is used to sense the positions of stars and generate signals corresponding to the positions of the stars as seen in its field of view. The star catalog contains star location data that is stored using a primary and multiple secondary arrays sorted by both declination (DEC) and right ascension (RA), respectively. The star location data stored in the star catalog is predetermined by calculating a plurality of desired star locations, associating one of a plurality of stars with each of the plurality of desired star locations based upon a neighborhood association angle to generate an associated plurality of star locations: If an artificial star gap occurs during association, then the neighborhood association angle for reassociation is increased. The controller uses the star catalog to determine which stars to select to provide star measurement residuals for correcting gyroscope bias and spacecraft attitude.

  6. DETERMINANTS OF CONSTRUCTION FOR AN INFORMATION SYSTEM SUPPORTING INNOVATION MANAGEMENT

    Directory of Open Access Journals (Sweden)

    Sabina Rokita

    2013-02-01

    Full Text Available Issues regarding information needs for managing innovation in a company are presented in the paper. The authors describe the concept of cost classification and practical solutions in typical reporting for assessing analysis of the efficiency of innovation activities in companies. The concept is depiced against the background of general issues related to internal factors which influence the system of innovation process management.

  7. Computer system for determination of cultural relic's age

    International Nuclear Information System (INIS)

    The computer is described in which thermoluminescent dosimeter is used for measuring ancient porcelain's age. The calculating formula of cultural relic's age, the working principle of the computer interface circuit and the design strategy of software are given. This system has been put into practical use for two years. The performance is stable and the operation is convenient. The calculation speed is raised as well as the calculation precision is guaranteed. All kinds of original data can be stored

  8. Determinants of quality management systems implementation in hospitals

    OpenAIRE

    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. Using the thesaurus terms 'Total Quality Management' and 'Quality Assurance Health Care'. combined with the term 'hospital' and 'implement*', we identified 533 publications. The screening process was b...

  9. Electrometric method to determine the surface impedance of an ice-sea water bilayer system

    Science.gov (United States)

    Bashkuev, Yu. B.; Naguslaeva, I. B.; Khaptanov, V. B.; Dembelov, M. G.

    2016-02-01

    An electrometric method to determine the surface impedance of an ice-sea water bilayer system is suggested. The complex impedance (its magnitude and phase) of this system is determined at very low, low, and medium frequencies from electrometric, rather than radio, measurements. For the ice-sea water system, it is sufficient to determine the conductivity and thickness of a water sample from drilling data.

  10. 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.

  11. Rapid earthquake magnitude determination for Vrancea early warning system

    International Nuclear Information System (INIS)

    Due to the huge amount of recorded data, an automatic procedure was developed and used to test different methods to rapidly evaluate earthquake magnitude from the first seconds of the P wave. In order to test all the algorithms involved in detection and rapid earthquake magnitude estimation, several tests were performed, in order to avoid false alarms. A special detection algorithm was developed, that is based on the classical STA/LTA algorithm and tuned for early warning purpose. A method to rapidly estimate magnitude in 4 seconds from detection of P wave in the epicenter is proposed. The method was tested on al recorded data, and the magnitude error determination is acceptable taking into account that it is computed from only 3 stations in a very short time interval. (author)

  12. RF system calibration for global Q matrix determination.

    Science.gov (United States)

    Padormo, Francesco; Beqiri, Arian; Malik, Shaihan J; Hajnal, Joseph V

    2016-06-01

    The use of multiple transmission channels (known as Parallel Transmission, or PTx) provides increased control of the MRI signal formation process. This extra flexibility comes at a cost of uncertainty of the power deposited in the patient under examination: the electric fields produced by each transmitter can interfere in such a way to lead to excessively high heating. Although it is not possible to determine local heating, the global Q matrix (which allows the whole-body Specific Absorption Rate (SAR) to be known for any PTx pulse) can be measured in-situ by monitoring the power incident upon and reflected by each transmit element during transmission. Recent observations have shown that measured global Q matrices can be corrupted by losses between the coil array and location of power measurement. In this work we demonstrate that these losses can be accounted for, allowing accurate global Q matrix measurement independent of the location of the power measurement devices. PMID:26747407

  13. Detection and kinetic studies of triplex formation by oligodeoxynucleotides using real-time biomolecular interaction analysis (BIA).

    OpenAIRE

    Bates, P. J.; Dosanjh, H. S.; S. Kumar; Jenkins, T. C.; Laughton, C A; Neidle, S

    1995-01-01

    Real-time biomolecular interaction analysis (BIA) has been applied to triplex formation between oligodeoxynucleotides. 5'-Biotinylated oligonucleotides were immobilised on the streptavidin-coated surface of a biosensor chip and subsequently hybridised to their complementary strand. Sequence-specific triplex formation was observed when a suitable third-strand oligopyrimidine was injected over the surface-bound duplex. In addition, a single-stranded oligonucleotide immobilised on the chip surfa...

  14. 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...

  15. 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

  16. Determining Esophageal Anatomy With A New Electroanatomical Mapping System

    Directory of Open Access Journals (Sweden)

    Diego Chemello MD

    2010-03-01

    Full Text Available A 53-year-old woman with symptomatic paroxysmal atrial fibrillation was referred for pulmonary vein isolation (PVI. After obtaining access to left atrium (LA and placement of catheters by standard technique, a high-resolution electroanatomical map of the LA and the pulmonary veins (PVs was constructed using a map catheter (EZ Steer® Bi-directional catheter, Biosense Webster, Inc. Diamond Bar, USA and the Carto® 3 System (Biosense-Webster Inc. Diamond Bar, USA in the Fast Anatomical Mapping (FAM mode.

  17. A Probabilistic Determination of Fuzzy System with Evaluation

    OpenAIRE

    Deepali Mahatma; Ankit Toshniwal; Rajesh Jatoliya; Pankaj Singh Parihar

    2013-01-01

    The term “fuzzy logic” is rather ambiguous because it refers to problems and method that belongs to different field of investigation. it is possible to find three meaning for the expression “fuzzy logic”. In its most popular acceptation, it refers to numerical computations based on fuzzy rules, for the purpose of modeling a control low in system engineering. Interestingly, the original motivation of fuzzy logic control was to represent expert knowledge in a rule based style and to build a sta...

  18. Determination of energy levels in organic bulk-heterojunction systems

    Energy Technology Data Exchange (ETDEWEB)

    Wetzstein, Holger; Krause, Stefan; Schoell, Achim; Reinert, Friedrich [Experimental Physics VII, Julius-Maximilians-University of Wuerzburg, D-97074 Wuerzburg (Germany); Liedtke, Moritz; Kern, Julia; Deibel, Carsten [Experimental Physics VI, Julius-Maximilians-University of Wuerzburg, D-97074 Wuerzburg (Germany)

    2010-07-01

    In order to improve the efficiency of electronic devices based on organic semiconducting materials the detailed knowledge about the exact position of the energy levels responsible for charge transport is crucial. The experimental determination is particularly complicated for bulk heterojunctions of p- and n-conducting materials in terms of sample preparation, film morphology and distinction of the different spectroscopic signatures. We investigated four promising materials for organic photovoltaic devices: the electron donor poly(3-hexylthiophene-2,5-diyl) (P3HT) and the three electron acceptors [6,6]-phenyl-C{sub 61} butyric acid methyl ester (PC{sub 60}BM), its bisadduct analogue (bis- PC{sub 60}BM) and [6,6]-phenyl-C{sub 71} butyric acid methyl ester (PC{sub 70}BM). Thin films of pristine materials as well as bulk heterojunction samples of P3HT:PC{sub 60}BM, P3HT:bis-PC{sub 60}BM and P3HT:PC{sub 70}BM were examined with respect to their valence levels using ultraviolet photoelectron spectroscopy (UPS).

  19. Climate system properties determining the social cost of carbon

    International Nuclear Information System (INIS)

    The choice of an appropriate scientific target to guide global mitigation efforts is complicated by uncertainties in the temperature response to greenhouse gas emissions. Much climate policy discourse has been based on the equilibrium global mean temperature increase following a concentration stabilization scenario. This is determined by the equilibrium climate sensitivity (ECS) which, in many studies, shows persistent, fat-tailed uncertainty. However, for many purposes, the equilibrium response is less relevant than the transient response. Here, we show that one prominent policy variable, the social cost of carbon (SCC), is generally better constrained by the transient climate response (TCR) than by the ECS. Simple analytic expressions show the SCC to be directly proportional to the TCR under idealized assumptions when the rate at which we discount future damage equals 2.8%. Using ensemble simulations of a simple climate model we find that knowing the true value of the TCR can reduce the relative uncertainty in the SCC substantially more, up to a factor of 3, than knowing the ECS under typical discounting assumptions. We conclude that the TCR, which is better constrained by observations, less subject to fat-tailed uncertainty and more directly related to the SCC, is generally preferable to the ECS as a single proxy for the climate response in SCC calculations. (letter)

  20. Climate system properties determining the social cost of carbon

    Science.gov (United States)

    Otto, Alexander; Todd, Benjamin J.; Bowerman, Niel; Frame, David J.; Allen, Myles R.

    2013-06-01

    The choice of an appropriate scientific target to guide global mitigation efforts is complicated by uncertainties in the temperature response to greenhouse gas emissions. Much climate policy discourse has been based on the equilibrium global mean temperature increase following a concentration stabilization scenario. This is determined by the equilibrium climate sensitivity (ECS) which, in many studies, shows persistent, fat-tailed uncertainty. However, for many purposes, the equilibrium response is less relevant than the transient response. Here, we show that one prominent policy variable, the social cost of carbon (SCC), is generally better constrained by the transient climate response (TCR) than by the ECS. Simple analytic expressions show the SCC to be directly proportional to the TCR under idealized assumptions when the rate at which we discount future damage equals 2.8%. Using ensemble simulations of a simple climate model we find that knowing the true value of the TCR can reduce the relative uncertainty in the SCC substantially more, up to a factor of 3, than knowing the ECS under typical discounting assumptions. We conclude that the TCR, which is better constrained by observations, less subject to fat-tailed uncertainty and more directly related to the SCC, is generally preferable to the ECS as a single proxy for the climate response in SCC calculations.

  1. Photoneutron logging system for direct uranium ore-grade determination

    International Nuclear Information System (INIS)

    A prototype photoneutron probe for direct uranium assay in exploratory boreholes has been built and field tested. An approx. 10-Ci 124Sb gamma-ray source together with a beryllium converter is used to produce neutrons that diffuse into the surrounding formation and cause fissions in any 235U present. The fission neutrons that return to the probe are energy analyzed and counted by a high-pressure helium detector, thus indicating the concentration of uranium. The response of the probe was measured in concrete models at the US Department of Energy (Grand Junction, Colorado) calibration facility and found to be approx. 35 counts/s for an 1% U3O8 concentration in an 11.4-cm-diam water-filled borehole (4.5 in.). The response is linear up to a concentration of at least 0.25% by weight U3O8. Effects resulting from changes in formation density, porosity, and neutron absorber content were also quantified, as well as the tool response as a function of borehole diameter and fluid. A logging vehicle was outfitted, and the photoneutron-based logging system was field tested at an exploration site near Canon City, Colorado. Logging data obtained in several open holes at this site are presented and compared to core chemical analyses and results obtained in the same holes using other logging methods. In about 1 month of field testing, the photoneutron-based uranium exploration system has proved to be simple to use and very reliable. 22 figures, 12 tables

  2. 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)

  3. 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. PMID:26643074

  4. 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.

  5. 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.

  6. Chemical and biomolecular characterization of Artemisia umbelliformis Lam., an important ingredient of the alpine liqueur "Genepi".

    Science.gov (United States)

    Rubiolo, Patrizia; Matteodo, Maura; Bicchi, Carlo; Appendino, Giovanni; Gnavi, Giorgio; Bertea, Cinzia; Maffei, Massimo

    2009-05-13

    Artemisia umbelliformis Lam., an important alpine plant used for the preparation of flavored beverages, showed a remarkable intraspecific variability, at both genomic and gene product (secondary metabolites) levels. The variability of A. umbelliformis Lam. currently cultivated in Piedmont (Italy, Au1) and in Switzerland (Au2) was investigated by combining the chemical analysis of essential oil and sesquiterpene lactones and the molecular characterization of the 5S-rRNA-NTS gene by PCR and PCR-RFLP. Marked differences were observed between the two plants. Au1 essential oil contained alpha- and beta-thujones as the main components, whereas Au2 contained 1,8-cineole, borneol, and beta-pinene. Au1 sesquiterpene lactone fractions contained cis-8-eudesmanolide derivatives and Au2 the trans-6-germacranolide costunolide. Specific A. umbelliformis Au1 and Au2 primers were designed on the sequence of the 5S-rRNA gene spacer region. Furthermore, a PCR-restriction fragment length polymorphism (PCR-RFLP) method was applied using RsaI and TaqI restriction enzymes. Chemical and biomolecular data contributed to the characterization of A. umbeliformis chemotypes. PMID:19326948

  7. Bio-objectifying European bodies: standardisation of biobanks in the Biobanking and Biomolecular Resources Research Infrastructure.

    Science.gov (United States)

    Tamminen, Sakari

    2015-01-01

    The article traces the genealogy of the Minimum Information About Biobank Data Sharing model, created in the European Biobanking and Biomolecular Resources Research Infrastructure to facilitate collaboration among biobanks and to foster the exchange of biological samples and data. This information model is aimed at the identification of biobanks; unification of databases; and objectification of the information, samples, and related studies - to create a completely new 'bio-object infrastructure' within the EU. The paper discusses key challenges in creating a 'universal' information model of such a kind, the most important technical translations of European research policy needed for a standardised model for biobank information, and how this model creates new bio-objects. The author claims that this amounts to redefinition of biobanks and technical governance over virtually bio-objectified European populations. It is argued here that old governance models based on the nation-state need radical reconsideration so that we are prepared for a new and changing situation wherein bodies of information that lack organs flow from one database to another with a click of a mouse. PMID:26626620

  8. Magneto-optical relaxation measurements for the characterization of biomolecular interactions

    International Nuclear Information System (INIS)

    Measurements of the magneto-optical relaxation of ferrofluids (MORFF) were applied as a novel homogeneous immunoassay for the investigation of biomolecular interactions. The technique is based on magnetic nanoparticles (MNP) functionalized with antibodies. The relaxation time of the optical birefringence that occurs when a pulsed magnetic field is applied to the nanoparticle suspension depends on the particle size. This enables the detection of particle aggregates formed after the addition of the antigen coupling partner. MORFF size measurements on the original ferrofluid and its fractions obtained by magnetic fractionation are comparable with results from other methods such as atomic force microscopy and photon correlation spectroscopy. In kinetic studies, the binding properties of five antigens and their polyclonal antibodies were investigated: human immunoglobulin G (hIgG), human immunoglobulin M (hIgM), human Eotaxin (hEotaxin), human carcinoembryonic antigen (hCEA), and human insulin (hInsulin). The enlargement of the relaxation time observed during the coupling experiments is expressed in terms of a size distribution function, which includes MNP monomers as well as aggregates. The kinetic process can be described by a model of stepwise polymerization. The kinetic parameters obtained are compared to results of surface plasmon resonance measurements

  9. 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. PMID:27160350

  10. 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.

  11. A new source for quantum optics with biomolecules and biomolecular clusters

    Science.gov (United States)

    Marksteiner, Markus; Haslinger, Philipp; Ulbricht, Hendrik; Arndt, Markus

    2008-03-01

    We present recent progress towards matter wave experiments with amino acids, polypeptides and large biomolecular clusters. All successful experiments on macromolecule interferometry so far, with fullerenes, fullerene derivates and large perfluoroalkyl-functionalized azobenzenes used effusive beam sources. The combination of Stark deflectometry with quantum interferometry also allowed us to create a new device for precisely measuring electric susceptibilities of large molecules in the gas phase. In order to apply quantum interference to molecules of biological interest, we have now implemented a pulsed laser desorption source. The combination of UV laser desorption into an intense noble gas jet and single-photon ionization by a VUV excimer laser (157nm) allows us to observe intense neutral jets of amino acids (e.g. Tryptophan), nucleotides (e.g. Guanin) and polypeptides ranging from tri-peptides to Gramicidin. Remarkably, we also found a new method for producing large neutral amino acid clusters, such as for instance Trp30, with masses exceeding 6000 amu: the addition of alkaline Earth salts in the desorption process leads to the inclusion of at least one metal atom per complex and is sufficient to catalyze the cluster formation process.

  12. An Atomic Force Microscope with Dual Actuation Capability for Biomolecular Experiments

    Science.gov (United States)

    Sevim, Semih; Shamsudhin, Naveen; Ozer, Sevil; Feng, Luying; Fakhraee, Arielle; Ergeneman, Olgaç; Pané, Salvador; Nelson, Bradley J.; Torun, Hamdi

    2016-06-01

    We report a modular atomic force microscope (AFM) design for biomolecular experiments. The AFM head uses readily available components and incorporates deflection-based optics and a piezotube-based cantilever actuator. Jetted-polymers have been used in the mechanical assembly, which allows rapid manufacturing. In addition, a FeCo-tipped electromagnet provides high-force cantilever actuation with vertical magnetic fields up to 0.55 T. Magnetic field calibration has been performed with a micro-hall sensor, which corresponds well with results from finite element magnetostatics simulations. An integrated force resolution of 1.82 and 2.98 pN, in air and in DI water, respectively was achieved in 1 kHz bandwidth with commercially available cantilevers made of Silicon Nitride. The controller and user interface are implemented on modular hardware to ensure scalability. The AFM can be operated in different modes, such as molecular pulling or force-clamp, by actuating the cantilever with the available actuators. The electromagnetic and piezoelectric actuation capabilities have been demonstrated in unbinding experiments of the biotin-streptavidin complex.

  13. 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

  14. The Effect of Biomolecular Gradients on Mesenchymal Stem Cell Chondrogenesis under Shear Stress

    Directory of Open Access Journals (Sweden)

    Alexander L. Rivera

    2015-03-01

    Full Text Available Tissue engineering is viewed as a promising option for long-term repair of cartilage lesions, but current engineered cartilage constructs fail to match the mechanical properties of native tissue. The extracellular matrix of adult human articular cartilage contains highly organized collagen fibrils that enhance the mechanical properties of the tissue. Unlike articular cartilage, mesenchymal stem cell (MSC based tissue engineered cartilage constructs lack this oriented microstructure and therefore display much lower mechanical strength. The goal of this study was to investigate the effect of biomolecular gradients and shear stress on MSCs undergoing chondrogenesis within a microfluidic device. Via poly(dimethyl siloxane soft-lithography, microfluidic devices containing a gradient generator were created. Human MSCs were seeded within these chambers and exposed to flow-based transforming growth factor β1 (TGF-β1 gradients. When the MSCs were both confluent and exposed to shear stress, the cells aligned along the flow direction. Exposure to TGF-β1 gradients led to chondrogenesis of MSCs, indicated by positive type II collagen staining. These results, together with a previous study that showed that aligned MSCs produce aligned collagen, suggest that oriented cartilage tissue structures with superior mechanical properties can be obtained by aligning MSCs along the flow direction and exposing MSCs to chondrogenic gradients.

  15. A computational study of the interaction of graphene structures with biomolecular units.

    Science.gov (United States)

    Carballeira, Diego López; Ramos-Berdullas, Nicolás; Pérez-Juste, Ignacio; Fajín, José Luis Cagide; Cordeiro, M Natália D S; Mandado, Marcos

    2016-06-01

    Due to the great interest that biochemical sensors constructed from graphene nanostructures have raised recently, in this work we analyse in detail the electronic factors responsible for the large affinity of biomolecular units for graphene surfaces using ab initio quantum chemical tools based on density functional theory. Both finite and periodic graphene structures have been employed in our study. Whereas the former allows the analysis of the different energy components contributing to the interaction energy separately, the periodic structure provides a more realistic calculation of the total adsorption energy in an extended graphene surface and serves to validate the results obtained using the finite model. In addition, qualitative relations between interaction energy and electron polarization upon adsorption have been established using the finite model. In this work, we have analysed thermodynamically stable adsorption complexes formed by glycine, melamine, pyronin cation, porphine, tetrabenzoporphine and phthalocyanine with a 2D structure of ninety six carbons and periodic structures formed by cells of fifty and seventy two carbons. Differences in the electrostatic, Pauli repulsion, induction and dispersion energies among aromatic and non-aromatic molecules, charged and non-charged molecules and H-π and stacking interactions have been thoroughly analysed in this work. PMID:27210053

  16. Determination of SMES capacity to enhance the dynamic stability of power system

    Energy Technology Data Exchange (ETDEWEB)

    Shi, J., E-mail: shijing_hust@126.co [R and D Center of Applied Superconductivity, Huazhong University of Science and Technology, Wuhan (China); Tang, Y. [R and D Center of Applied Superconductivity, Huazhong University of Science and Technology, Wuhan (China); Dai, T. [Department of Information and Electrical Engineering, Shandong University of Science and Technology , Qingdao (China); Ren, L.; Li, J.; Cheng, S. [R and D Center of Applied Superconductivity, Huazhong University of Science and Technology, Wuhan (China)

    2010-11-01

    This paper proposes the principle of SMES capacity determination for power system stable operation. Adopting the energy function method, the mechanism of SMES damping power oscillation in the classical single-machine infinite-bus (SMIB) system is analyzed. The released kinetic energy during disturbance is the original of power system oscillation, which is taken as the principle of SMES capacity determination. Then, the influence of fault type, fault position, and fault clearing time on the SMES capacity determination are discussed. Using MATLAB simulation, the principle of SMES capacity determination is evaluated.

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

    DEFF Research Database (Denmark)

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

    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 and in...

  18. Metallic Glass Wire Based Localization of Kinesin/Microtubule Bio-molecular Motility System

    Science.gov (United States)

    Kim, K.; Sikora, A.; Yaginuma, S.; Nakayama, K. S.; Nakazawa, H.; Umetsu, M.; Hwang, W.; Teizer, W.

    2014-03-01

    We report electrophoretic accumulation of microtubules along metallic glass (Pd42.5Cu30Ni7.5P20) wires free-standing in solution. Microtubules are dynamic cytoskeletal filaments. Kinesin is a cytoskeletal motor protein. Functions of these bio-molecules are central to various dynamic cellular processes. Functional artificial organization of bio-molecules is a prerequisite for transferring their native functions into device applications. Fluorescence microscopy at the individual-microtubule level reveals microtubules aligning along the wire axis during the electrophoretic migration. Casein-treated electrodes are effective for releasing trapped microtubules upon removal of the external field. Furthermore, we demonstrate gliding motion of microtubules on kinesin-treated metallic glass wires. The reversible manner in the local adsorption of microtubules, the flexibility of wire electrodes, and the compatibility between the wire electrode and the bio-molecules are beneficial for spatio-temporal manipulation of the motility machinery in 3 dimensions.

  19. Computational Modeling of Biomolecular Systems: Insights Into Protein Dynamics, Free Energy and Peptide/Ligand Binding

    OpenAIRE

    Huang, Yu-ming Mindy

    2014-01-01

    The opening of the 21st century has been marked as a generation of biological science. Nowadays, the understanding of the sequence and structure of biomolecules is growing rapidly. And researchers from multiple disciplines, chemistry, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. The state-of-the-art techniques of computational chemistry and molecular modeling can be applied to study a wide range of chemical and bio...

  20. 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.

  1. 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.

  2. Fluid dynamics modeling for synchronizing surface plasmon resonance and quartz crystal microbalance as tools for biomolecular and targeted drug delivery studies.

    Science.gov (United States)

    Viitala, Tapani; Liang, Huamin; Gupta, Mayur; Zwinger, Thomas; Yliperttula, Marjo; Bunker, Alex

    2012-07-15

    We have used computational fluid dynamics modeling (CFD) to synchronize the flow conditions in the flow channels of two complementary surface-sensitive characterization techniques: surface plasmon resonance (SPR) and quartz crystal microbalance (QCM). Since the footprint of the flow channels of the two devices is specified by their function, the flow behavior can only be varied either by altering the height of the flow channel, or altering the volumetric rate of flow (flow rate) through the channel. The relevant quantity that must be calibrated is the shear strain on the measurement surface (center and bottom) of the flow channel. Our CFD modeling shows that the flow behavior is in the Stokes flow regime. We were thus able to generate a scaling expression with parameters for flow rate and flow channel height for each of the two devices: f(QCM)=2.64f(SPR)(h(QCM)/h(SPR)(2), where f(QCM) and f(SPR) are the flow rates in the SPR and QCM flow channels, respectively, and h(QCM)/h(SPR) is the ratio of the heights of the two channels. We demonstrate the success of our calibration procedure through the combined use of commercially available SPR and QCM flow channel devices on both a biomolecular interaction system of surface immobilized biotin and streptavidin and a targeted drug delivery model system of biotinylated liposomes interacting with a streptavidin functionalized surface. PMID:22579516

  3. Methodology and key determinants of building an efficient national innovation system of a country

    OpenAIRE

    Viktoriia Gurova

    2015-01-01

    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...

  4. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    Science.gov (United States)

    Doster, W.; Nakagawa, H.; Appavou, M. S.

    2013-07-01

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td.

  5. Development of a biomolecular assay for postmortem diagnosis of Taenia saginata Cysticercosis.

    Science.gov (United States)

    Chiesa, Francesco; Dalmasso, Alessandra; Bellio, Alberto; Martinetti, Manuela; Gili, Stefano; Civera, Tiziana

    2010-10-01

    Bovine cysticercosis is caused by the larval stage of the human tapeworm Taenia saginata. According to European data on meat inspection, the prevalence ranges from 0.007% to 6.8%, but the real prevalence is considered to be at least 10 times higher. Laboratory confirmation of the etiological agent is based on gross, stereomicroscopic, and histological examination of submitted specimens. False identifications may occur, possibly because of death and degeneration of cysts, or because taeniid larvae and other tissue parasites, such as Sarcocystis spp., may cause similar macroscopic morphological lesions. Therefore, tests that can warrant sure identification of taeniid lesions and calcified cysts in the muscle are needed. The focus of our study was to develop a suitable postmortem test that could be applied on putative lesions by T. saginata cysticerci, as ambiguously diagnosed after routine meat inspection. In particular, we proposed a biomolecular assay targeting the mitochondrial cytochrome c oxidase subunit I gene (COI). For developing the polymerase chain reaction assay, viable cysts of Cysticercus bovis (n = 10) were used as positive reference samples, and those of Echinococcus granulosus (n = 3), Cysticercus tenuicollis (n = 3), and Sarcocystis spp. (n = 4) as reference negative controls. Further, to evaluate the applicability of the proposed assay, 171 samples of bovine muscular tissue, obtained from local slaughterhouses and containing lesions recognized as T. saginata cysticerci by macroscopic examination, were tested. The proposed test confirmed the diagnosis at postmortem inspection in 94.7% (162/171) of samples. In conclusion, the assay developed in this study, amplifying a short fragment from the mitochondrial gene COI, showed to be suitable for samples containing both viable and degenerating T. saginata cysticerci, yielding an unequivocal diagnosis. PMID:20618079

  6. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    Energy Technology Data Exchange (ETDEWEB)

    Doster, W. [Physik-Department, Technische Universität München, D-85748 Garching (Germany); Nakagawa, H. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany); Japan Atomic Energy Agency, Quantum Beam Science Directorate, Tokai, Ibaraki 319-1195 (Japan); Appavou, M. S. [Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at MLZ, Lichtenbergstraße 1, 85747 Garching (Germany)

    2013-07-28

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at T{sub d} from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature T{sub g}. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature T{sub d}.

  7. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments

    International Nuclear Information System (INIS)

    Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and/or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td

  8. 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.

  9. RCSLK9: reactor coolant system leak rate determination for PWRs. User's guide

    International Nuclear Information System (INIS)

    RCSLK9 is a computer program that was developed to analyze the leak tightness of the primary cooling system for any pressurized water reactor. From system conditions, water levels in tanks, and certain system design parameters, RCSLK9 calculates the loss of water from the cooling system and the increase of water in the leakage collection system during an arbitrary time interval. The program determines the system leak rates and displays or prints a report of the results. For initial application of the program at a reactor, RCSLK9 creates a file of system parameters and stores it for future use. RCSLK9 is written for use on the IBM PC

  10. BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

    International Nuclear Information System (INIS)

    We describe the role of the BioMagResBank (BMRB) within the Worldwide Protein Data Bank (wwPDB) and recent policies affecting the deposition of biomolecular NMR data. All PDB depositions of structures based on NMR data must now be accompanied by experimental restraints. A scheme has been devised that allows depositors to specify a representative structure and to define residues within that structure found experimentally to be largely unstructured. The BMRB now accepts coordinate sets representing three-dimensional structural models based on experimental NMR data of molecules of biological interest that fall outside the guidelines of the Protein Data Bank (i.e., the molecule is a peptide with 23 or fewer residues, a polynucleotide with 3 or fewer residues, a polysaccharide with 3 or fewer sugar residues, or a natural product), provided that the coordinates are accompanied by representation of the covalent structure of the molecule (atom connectivity), assigned NMR chemical shifts, and the structural restraints used in generating model. The BMRB now contains an archive of NMR data for metabolites and other small molecules found in biological systems

  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. 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...

  13. Method of determining remedial control actions for a power system in an insecure state

    DEFF Research Database (Denmark)

    2013-01-01

    determined comprising a scheme for re-dispatching power generation for each unsafe generator to thereby establish a secure operating condition for the power system.A new safe operating point in the impedance plane for each unsafe generator may be determined, and a distance between the generator injection......A method of determining remedial control actions for a power system in an insecure and unstable operating condition is provided. The power system has a plurality of generators injecting power into a network and each generator has a generator injection impedance and a stability boundary in the...... injection impedance plane. A system safety boundary is calculated based on a predetermined network operating safety margin for each generator, the generator injection impedance is compared with the safety boundary and it is determined whether each generator is safe or unsafe. A remedial control action is...

  14. A teaching and learning sequence about the interplay of chance and determinism in nonlinear systems

    International Nuclear Information System (INIS)

    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 secondary students' capabilities and difficulties in understanding the scientific point of view were investigated, using a teaching experiment design. The results show that most students were capable of sound explanations concerning the interplay of chance and determinism in nonlinear systems

  15. Evaluation of kinetic constants of biomolecular interaction on optical surface plasmon resonance sensor with Newton Iteration Method

    Science.gov (United States)

    Zhao, Yuanyuan; Jiang, Guoliang; Hu, Jiandong; Hu, Fengjiang; Wei, Jianguang; Shi, Liang

    2010-10-01

    In the immunology, there are two important types of biomolecular interaction: antigens-antibodies and receptors-ligands. Monitoring the response rate and affinity of biomolecular interaction can help analyze the protein function, drug discover, genomics and proteomics research. Moreover the association rate constant and dissociation rate constant of receptors-ligands are the important parameters for the study of signal transmission between cells. Recent advances in bioanalyzer instruments have greatly simplified the measurement of the kinetics of molecular interactions. Non-destructive and real-time monitoring the response to evaluate the parameters between antigens and antibodies can be performed by using optical surface plasmon resonance (SPR) biosensor technology. This technology provides a quantitative analysis that is carried out rapidly with label-free high-throughput detection using the binding curves of antigens-antibodies. Consequently, the kinetic parameters of interaction between antigens and antibodies can be obtained. This article presents a low cost integrated SPR-based bioanalyzer (HPSPR-6000) designed by ourselves. This bioanalyzer is mainly composed of a biosensor TSPR1K23, a touch-screen monitor, a microprocessor PIC24F128, a microflow cell with three channels, a clamp and a photoelectric conversion device. To obtain the kinetic parameters, sensorgrams may be modeled using one of several binding models provided with BIAevaluation software 3.0, SensiQ or Autolab. This allows calculation of the association rate constant (ka) and the dissociation rate constant (kd). The ratio of ka to kd can be used to estimate the equilibrium constant. Another kind is the analysis software OriginPro, which can process the obtained data by nonlinear fitting and then get some correlative parameters, but it can't be embedded into the bioanalyzer, so the bioanalyzer don't support the use of OriginPro. This paper proposes a novel method to evaluate the kinetic parameters

  16. 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.

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

    International Nuclear Information System (INIS)

    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.

  18. 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...

  19. Evaluation of five miniature chromatography systems for determining labeling efficiency of technetium Tc 99m pentetate.

    Science.gov (United States)

    Robbins, P J

    1983-04-01

    The reliability and reproducibility of five miniature chromatography systems for the radiochemical purity of 99mTc-labeled technetium Tc 99m pentetate was evaluated. Radiochemical purity of technetium Tc 99m pentetate was determined 15-30 minutes after preparation once a month for nine consecutive months. A reference value was determined by gel filtration or by conventional-length paper chromatography and thin-layer chromatography. Radiochemical purity was determined simultaneously by five miniature chromatography systems. The miniature systems included an in-house system and commercial systems distributed by Ackerman Nuclear, Ashley Innovations, Atomic Products, and Technical Advancement. Each miniature system was tested in duplicate. A follow-up comparison of the Ackerman Nuclear and in-house systems was performed for an additional nine months. Labeling efficiency by the reference method was greater than 97% for all nine months. The miniature systems gave results that were comparable in most months. Very low labeling efficiency occurred with the Ackerman Nuclear system in month 9. The follow-up comparison produced only one unconfirmed result for the Ackerman Nuclear system that would have caused a laboratory to erroneously discard a batch of technetium Tc 99m pentetate. The miniature chromatography systems evaluated generally will give reliable and reproducible results for the radiochemical purity of technetium Tc 99m pentetate for nine months after receipt of the systems. PMID:6342380

  20. Evaluation of five miniature chromatography systems for determining labeling efficiency of technetium Tc 99m pentetate

    International Nuclear Information System (INIS)

    The reliability and reproducibility of five miniature chromatography systems for the radiochemical purity of 99mTc-labeled technetium Tc 99m pentetate was evaluated. Radiochemical purity of technetium Tc 99m pentetate was determined 15-30 minutes after preparation once a month for nine consecutive months. A reference value was determined by gel filtration or by conventional-length paper chromatography and thin-layer chromatography. Radiochemical purity was determined simultaneously by five miniature chromatography systems. The miniature systems included an in-house system and commercial systems distributed by Ackerman Nuclear, Ashley Innovations, Atomic Products, and Technical Advancement. Each miniature system was tested in duplicate. A follow-up comparison of the Ackerman Nuclear and in-house systems was performed for an additional nine months. Labeling efficiency by the reference method was greater than 97% for all nine months. The miniature systems gave results that were comparable in most months. Very low labeling efficiency occurred with the Ackerman Nuclear system in month 9. The follow-up comparison produced only one unconfirmed result for the Ackerman Nuclear system that would have caused a laboratory to erroneously discard a batch of technetium Tc 99m pentetate. The miniature chromatography systems evaluated generally will give reliable and reproducible results for the radiochemical purity of technetium Tc 99m pentetate for nine months after receipt of the systems

  1. 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).

  2. An automatic system for acidity determination based on sequential injection titration and the monosegmented flow approach.

    Science.gov (United States)

    Kozak, Joanna; Wójtowicz, Marzena; Gawenda, Nadzieja; Kościelniak, Paweł

    2011-06-15

    An automatic sequential injection system, combining monosegmented flow analysis, sequential injection analysis and sequential injection titration is proposed for acidity determination. The system enables controllable sample dilution and generation of standards of required concentration in a monosegmented sequential injection manner, sequential injection titration of the prepared solutions, data collecting, and handling. It has been tested on spectrophotometric determination of acetic, citric and phosphoric acids with sodium hydroxide used as a titrant and phenolphthalein or thymolphthalein (in the case of phosphoric acid determination) as indicators. Accuracy better than |4.4|% (RE) and repeatability better than 2.9% (RSD) have been obtained. It has been applied to the determination of total acidity in vinegars and various soft drinks. The system provides low sample (less than 0.3 mL) consumption. On average, analysis of a sample takes several minutes. PMID:21641455

  3. Profitability of Western European banking systems: panel evidence on structural and cyclical determinants

    OpenAIRE

    Beckmann, Rainer

    2007-01-01

    This paper analyses structural and cyclical determinants of banking profitability in 16 Western European countries. We find that financial structure matters, particularly through the beneficial effect of the capital market orientation in the respective national financial system. Furthermore, higher diversification regarding banks' income sources shows a positive effect. The industry concentration of national banking systems, though, does not significantly affect aggregate profitability. Busin...

  4. ON THE PROBLEM WITH DETERMINATION OF COOLING SYSTEM PARAMETERS IN MOBILE VEHICLE ENGINES

    Directory of Open Access Journals (Sweden)

    A. Yakubovich

    2014-10-01

    Full Text Available The paper proposes a methodology for determination of fluid and air contour parameters of cooling systems in mobile vehicle engines that permits to calculate a cooling system, to analyze influence of heat carrier expendable parameters on a temperature mode, surfaces of radiator cooling, and also temperature of heat-carriers and environment. 

  5. 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...

  6. ON THE PROBLEM WITH DETERMINATION OF COOLING SYSTEM PARAMETERS IN MOBILE VEHICLE ENGINES

    OpenAIRE

    A. Yakubovich; Tarasenko, V.

    2014-01-01

    The paper proposes a methodology for determination of fluid and air contour parameters of cooling systems in mobile vehicle engines that permits to calculate a cooling system, to analyze influence of heat carrier expendable parameters on a temperature mode, surfaces of radiator cooling, and also temperature of heat-carriers and environment. 

  7. The Determination of Heat Capacity Ratios in a Simple Open System

    Science.gov (United States)

    Holden, Glen L.

    2007-01-01

    A virtually closed system is treated as open and compared to known results. The classic experiment of Clement and Desormes provides the conceptual framework for this open system approach in determining the molar heat capacity ratios, lambda. This alternate view, extends the theoretical treatment beyond the first law of thermodynamics for closed…

  8. 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

  9. Bend-twist-stretch model for coarse elastic network simulation of biomolecular motion

    Science.gov (United States)

    Stember, Joseph N.; Wriggers, Willy

    2009-08-01

    The empirical harmonic potential function of elastic network models (ENMs) is augmented by three- and four-body interactions as well as by a parameter-free connection rule. In the new bend-twist-stretch (BTS) model the complexity of the parametrization is shifted from the spatial level of detail to the potential function, enabling an arbitrary coarse graining of the network. Compared to distance cutoff-based Hookean springs, the approach yields a more stable parametrization of coarse-grained ENMs for biomolecular dynamics. Traditional ENMs give rise to unbounded zero-frequency vibrations when (pseudo)atoms are connected to fewer than three neighbors. A large cutoff is therefore chosen in an ENM (about twice the average nearest-neighbor distance), resulting in many false-positive connections that reduce the spatial detail that can be resolved. More importantly, the required three-neighbor connectedness also limits the coarse graining, i.e., the network must be dense, even in the case of low-resolution structures that exhibit few spatial features. The new BTS model achieves such coarse graining by extending the ENM potential to include three-and four-atom interactions (bending and twisting, respectively) in addition to the traditional two-atom stretching. Thus, the BTS model enables reliable modeling of any three-dimensional graph irrespective of the atom connectedness. The additional potential terms were parametrized using continuum elastic theory of elastic rods, and the distance cutoff was replaced by a competitive Hebb connection rule, setting all free parameters in the model. We validate the approach on a carbon-alpha representation of adenylate kinase and illustrate its use with electron microscopy maps of E. coli RNA polymerase, E. coli ribosome, and eukaryotic chaperonin containing T-complex polypeptide 1, which were difficult to model with traditional ENMs. For adenylate kinase, we find excellent reproduction (>90% overlap) of the ENM modes and B factors

  10. Determination of simplexes of mutual systems on the base of conversion figures by the matrix method

    International Nuclear Information System (INIS)

    New determination method of salt composition of singular and nonequilibrium stars simplexes of mutual systems of the 2 parallel n and n parallel 2 series, based on the introduction of the conversion figure in the matrix of mutual pairs of the salts, is described. Exclusion of the complex geometrical constructions increases expressiveness and availability of multicomponent systems investigation. The method is graphic particularly for determination of power-consuming simplexes, i. e. the salt compositions, Oaving the greatest values of reaction heats. Na, K, Ba parallel F, MoO4 system is considered

  11. Development of an automated optical inspection system for determining percent area coverage for spacecraft contamination control

    Science.gov (United States)

    Hogue, Patrick; Coopersmith, Jonathan D.

    2004-10-01

    This paper describes the use of an automated optical inspection system to determine the percent area coverage of particle matter on surfaces for determination of surface cleanliness in accordance with IEST-STD-CC1246 (formerly MIL-STD-1246). This system consists of an optical microscope, motor-driven X-Y stage, digital camera, and software and can be used to scan surfaces for particles with selected features; an example will be given of a scan for glass beads on Gel-Pak surfaces used to tape-lift spacecraft structure prior to shipment to a propulsion system supplier who prohibits glass beads from entering their facility.

  12. Precision Attitude Determination System (PADS) design and analysis. Two-axis gimbal star tracker

    Science.gov (United States)

    1973-01-01

    Development of the Precision Attitude Determination System (PADS) focused chiefly on the two-axis gimballed star tracker and electronics design improved from that of Precision Pointing Control System (PPCS), and application of the improved tracker for PADS at geosynchronous altitude. System design, system analysis, software design, and hardware design activities are reported. The system design encompasses the PADS configuration, system performance characteristics, component design summaries, and interface considerations. The PADS design and performance analysis includes error analysis, performance analysis via attitude determination simulation, and star tracker servo design analysis. The design of the star tracker and electronics are discussed. Sensor electronics schematics are included. A detailed characterization of the application software algorithms and computer requirements is provided.

  13. Ubiquitous Positioning: A Taxonomy for Location Determination on Mobile Navigation System

    CERN Document Server

    Bejuri, Wan Mohd Yaakob Wan; Sapri, Maimunah; 10.5121/sipij.2011.2103

    2011-01-01

    The location determination in obstructed area can be very challenging especially if Global Positioning System are blocked. Users will find it difficult to navigate directly on-site in such condition, especially indoor car park lot or obstructed environment. Sometimes, it needs to combine with other sensors and positioning methods in order to determine the location with more intelligent, reliable and ubiquity. By using ubiquitous positioning in mobile navigation system, it is a promising ubiquitous location technique in a mobile phone since as it is a familiar personal electronic device for many people. However, as research on ubiquitous positioning systems goes beyond basic methods there is an increasing need for better comparison of proposed ubiquitous positioning systems. System developers are also lacking of good frameworks for understanding different options during building ubiquitous positioning systems. This paper proposes taxonomy to address both of these problems. The proposed taxonomy has been constr...

  14. 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. Graphical Abstract Application of Hg speciation and the isotopic signature of Hg to enhance our understanding of the roles of Hg in metabolic, toxicological, and environmental processes. PMID:26753975

  15. A simple knowledge-based mining method for exploring hidden key molecules in a human biomolecular network

    Directory of Open Access Journals (Sweden)

    Tsuji Shingo

    2012-09-01

    Full Text Available Abstract Background In the functional genomics analysis domain, various methodologies are available for interpreting the results produced by high-throughput biological experiments. These methods commonly use a list of genes as an analysis input, and most of them produce a more complicated list of genes or pathways as the results of the analysis. Although there are several network-based methods, which detect key nodes in the network, the results tend to include well-studied, major hub genes. Results To mine the molecules that have biological meaning but to fewer degrees than major hubs, we propose, in this study, a new network-based method for selecting these hidden key molecules based on virtual information flows circulating among the input list of genes. The human biomolecular network was constructed from the Pathway Commons database, and a calculation method based on betweenness centrality was newly developed. We validated the method with the ErbB pathway and applied it to practical cancer research data. We were able to confirm that the output genes, despite having fewer edges than major hubs, have biological meanings that were able to be invoked by the input list of genes. Conclusions The developed method, named NetHiKe (Network-based Hidden Key molecule miner, was able to detect potential key molecules by utilizing the human biomolecular network as a knowledge base. Thus, it is hoped that this method will enhance the progress of biological data analysis in the whole-genome research era.

  16. Real-time and label-free detection of biomolecular interactions by oblique-incidence reflectivity difference method

    Science.gov (United States)

    Wang, Xu; Lu, Heng; Dai, Jun; Wen, Juan; Yuan, Kun; Lü, Hui-Bin; Jin, Kui-Juan; Zhou, Yue-Liang; Yang, Guo-Zhen

    2011-01-01

    We successfully conduct the label-free and real-time detection of the interactions between epoxy groups and rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide, and between the hybridization of 5' CTT CAG GTC ATG AGC CTG AT 3' and its complementary 3' GAA GTC CAG TAC TCG GAC TA 5' oligonucleotide, by the oblique-incidence reflectivity difference (OI-RD) method. The dynamic curves of OI-RD signals, corresponding to the kinetic processes of biomolecular combination or hybridization, are acquired. In our case, the combination of epoxy groups with rabbit IgG and 5' CTT CAG GTC ATG AGC CTG AT 3' oligonucleotide need almost one and a half hours and about two hundred seconds, respectively; and the hybridization of the two oligonucleotides needs about five hundred seconds. The experimental results show that the OI-RD is a promising method for the real-time and label-free detection of biomolecular interactions.

  17. Bioactive membranes for bone regeneration applications: effect of physical and biomolecular signals on mesenchymal stem cell behavior.

    Science.gov (United States)

    Tejeda-Montes, Esther; Smith, Katherine H; Rebollo, Elena; Gómez, Raúl; Alonso, Matilde; Rodriguez-Cabello, J Carlos; Engel, Elisabeth; Mata, Alvaro

    2014-01-01

    This study focuses on the in vitro characterization of bioactive elastin-like recombinamer (ELR) membranes for bone regeneration applications. Four bioactive ELRs exhibiting epitopes designed to promote mesenchymal stem cell adhesion (RGDS), endothelial cell adhesion (REDV), mineralization (HAP), and both cell adhesion and mineralization (HAP-RGDS) were synthesized using standard recombinant protein techniques. The materials were then used to fabricate ELR membranes incorporating a variety of topographical micropatterns including channels, holes and posts. Primary rat mesenchymal stem cells (rMSCs) were cultured on the different membranes and the effects of biomolecular and physical signals on cell adhesion, morphology, proliferation, and differentiation were evaluated. All results were analyzed using a custom-made MATLAB program for high throughput image analysis. Effects on cell morphology were mostly dependent on surface topography, while cell proliferation and cell differentiation were largely dependent on the biomolecular signaling from the ELR membranes. In particular, osteogenic differentiation (evaluated by staining for the osteoblastic marker osterix) was significantly enhanced on cells cultured on HAP membranes. Remarkably, cells growing on membranes containing the HAP sequence in non-osteogenic differentiation media exhibited significant up-regulation of the osteogenic marker as early as day 5, while those growing on fibronectin-coated glass in osteogenic differentiation media did not. These results are part of our ongoing effort to develop an optimized molecularly designed periosteal graft. PMID:24035887

  18. Institutional and Cultural Determinants of National VET Systems : Problems arising with the European Qualifications Framework (EQF)

    OpenAIRE

    Deißinger, Thomas

    2008-01-01

    The focus of this paper is on cultural patterns determining national VET systems and policies around the world. Within established typologies VET systems are normally distinguished by referring to institutions and steering mechanisms. However, behind these, cultural patterns underlie both the practice and the theory as well as the policy of VET in various countries. Specific problems arise when it comes to "harmonising" VET systems "through the backdoor". One of the current supranational inst...

  19. 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...

  20. 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.

  1. A Systems Study to Determine the Attractiveness of Solar System Bodies and Sites for Eventual Human Exploration

    Science.gov (United States)

    Andringa, Jason M.; Gray, Andrew A.

    2005-01-01

    A pre-phase A idea-generation team at the Jet Propulsion Laboratory (JPL), has conducted a study to rank all locations in the solar system based on attractiveness for human exploration. The process used to perform the study was composed of the following primary steps: determination of criteria (including value, cost, and risk criteria) upon which to rate sites in the solar system; weighting of the criteria based upon importance to eventual human exploration; selection of sites to consider and assignment of team members to the task of advocating the benefits of particular sites; rating the sites in both the short- and longterm based on team member presentations and team discussions; compilation of a score based on criteria weights and individual ratings. Finally a comparison of the total scores of different sites was completed to determine a ranking of all the bodies and sites in the solar system. Sensitivity analysis was also performed to determine how weightings affect the rankings.

  2. Cost of photovoltaic energy systems as determined by balance-of-system costs

    Science.gov (United States)

    Rosenblum, L.

    1978-01-01

    The effect of the balance-of-system (BOS), i.e., the total system less the modules, on photo-voltaic energy system costs is discussed for multikilowatt, flat-plate systems. Present BOS costs are in the range of 10 to 16 dollars per peak watt (1978 dollars). BOS costs represent approximately 50% of total system cost. The possibility of future BOS cost reduction is examined. It is concluded that, given the nature of BOS costs and the lack of comprehensive national effort focussed on cost reduction, it is unlikely that BOS costs will decline greatly in the next several years. This prognosis is contrasted with the expectations of the Department of Energy National Photovoltaic Program goals and pending legislation in the Congress which require a BOS cost reduction of an order of magnitude or more by the mid-1980s.

  3. Production and detection of neutral molecular beams : from single amino acids to biomolecular complexes

    International Nuclear Information System (INIS)

    biomolecular complexes. The largest observed complex is a gramicidin tetramer with a mass of 7,536amu. Furthermore, desorption of tryptophan together with alkaline earth salts, such as calcium-carbonate results in the formation of two different kinds of massive tryptophan clusters: Tryptophan clusters containing a single calcium atom with a mass of up to 6,800amu and also pure clusters with a mass of up to 7,100amu are observed. The inclusion of a metal atom into tryptophan clusters is observed also for strontium, barium ,sodium and copper. The cluster formation is studied additionally for other amino acids such as phenylalanine, the tripeptide tyrosine-tryptophan-glycine and the nucleotide guanine. The cluster formation between two different molecular species was observed after the simultaneous desorption of gramicidin and tryptophan and resulted in the attachment of tryptophan molecules to a single gramicidin. An alternative detection method to photo-ionization is examined by testing a superconducting single photon detector (SSPD) for its ability to detect individual neutral molecules. The sensitivity of the nanostructured SSPD seems not to be limited to small molecules. The superconducting detector is able to record velocity distributions of neutral insulin (∼5,700amu), myoglobin(∼17 kDa) and hemoglobin (∼66 kDa) beams. A check if the intact molecules leave the source is missing due to the lack of alternative detection methods for these molecules. The working principle of the SSPD relies on the fact, that an impinging particle leads to a breakdown of superconductivity. Further developments of the SSPD appear possible and promising in order to increase the mass range of detected neutral organic molecules, which cannot be detected in photo-ionization. The source is developed in order to fulfil the criteria needed for a combination with a Talbot-Lau interferometer. Interference of biomolecules is, beside the prove of the wave-particle duality, interesting for the

  4. 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.

  5. Application of expert systems for determination of machining parameters in milling operations

    Science.gov (United States)

    Tolouei-Rad, M.; Bidhendi, Essie

    1995-08-01

    An expert system has been developed which is capable of selecting appropriate cutting tools and determining required machining parameters for milling operations. One feature of this system which distinguishes it from conventional applications of expert systems is that it uses information stored in database files. This causes the existence of a limited umber of expertise rules stored in the knowledge base; bringing up the advantage of shorter running time for the system. Another advantage of this system is its ability to retrieve required information from computer-aided design (CAD) systems through an input file, run the program, and restore the resulting information in an output file without any user interaction. These advantages make it an ideal system to be used in computer-aided design and manufacturing (CAD/CAM) systems.

  6. Precision Attitude Determination System (PADS) system design and analysis: Single-axis gimbal star tracker

    Science.gov (United States)

    1974-01-01

    The feasibility is evaluated of an evolutionary development for use of a single-axis gimbal star tracker from prior two-axis gimbal star tracker based system applications. Detailed evaluation of the star tracker gimbal encoder is considered. A brief system description is given including the aspects of tracker evolution and encoder evaluation. System analysis includes evaluation of star availability and mounting constraints for the geosynchronous orbit application, and a covariance simulation analysis to evaluate performance potential. Star availability and covariance analysis digital computer programs are included.

  7. 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

    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......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......, 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 to...

  8. Determination of relaxation constants of multi-level quadrupole spin-system

    International Nuclear Information System (INIS)

    Possibility to determine relaxation constants of multi-level spin-system all single-quantum transitions under two-frequency effect is studied. By means of two-frequency nuclear quadrupole resonance one determines the times of relaxation for all single-quantum transitions of multi-level quadrupole spin-system on the basis of data on one transition. In this case, the accuracy of determination is equal to the accuracy of measurement of the relaxation times under single-frequency excitation of transition that is taken as a base one. Paper presents data on measurement and determination of relaxation constants using NQR technique in KReO4, NaReO4, as well as, in SbCl3, SbBr3 and in their complexes under various temperatures

  9. Unpacking Business Intelligence Systems Adoption Determinants: An Exploratory Study of Small and Medium Enterprises

    OpenAIRE

    Borut Puklavec; Tiago Oliveira; Aleš Popovič

    2015-01-01

    While extant business intelligence systems (BIS) adoption research focused mainly on adoption of BIS in large-sized organizations, our understanding about the adoption determinants and the process within small and medium enterprises (SME) is still limited. The aim of our research is to identify SME-specific determinants of BIS adoption at firm level that will guide the development and testing of a BIS adoption framework in the milieu of SMEs. By leveraging semi-structured interviews involving...

  10. SIMULTANEOUS DETERMINATION OF CHLORINE DIOXIDE AND HYPOCHLOROUS ACID IN BLEACHING SYSTEM

    OpenAIRE

    Qiang Wang; Kefu Chen; Jun Li Mail; Jun Xu; Shanshan Liu Mail

    2011-01-01

    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 wavelen...

  11. Using Vibration Analysis to Determine Refrigerant Levels In an Automotive Air Conditioning System

    OpenAIRE

    Stasiunas, Eric Carl

    2002-01-01

    Presently, auto manufacturers do not have do not have efficient or accurate methods to determine the amount of refrigerant (R-134a) in an air conditioning system of an automobile. In the research presented, vibration analysis is examined as a possible method to determine this R-134a amount. Initial laboratory tests were completed and experimental modal analysis methods were investigated. This approach is based on the hypothesis that the natural frequency of the accumulator bott...

  12. Determination of tributyl phosphate (TBP) by precision densimetry : TBP-varsol-HNO/sub 3/ system

    Energy Technology Data Exchange (ETDEWEB)

    Matsuda, H.T.; Araujo, B.F. de; Araujo, J.A. de (Instituto de Pesquisas Energeticas e Nucleares, Sao Paulo (Brazil). Centro de Engenharia Quimica)

    1980-01-01

    A simple and rapid method for TBP direct determination is presented, based on precision densimetry, aiming to control solvent concentration in the TBP-Varsol system during the reprocessing of irradiated uranium. The method comprises the determination of the density of liquids or gases by electronic measurement of the variation in the frequency (f) or period (T = 1/f) of a glass oscillator containing the liquid or the gas.

  13. System identification approach for determining flight dynamical characteristics of an airship from flight data

    OpenAIRE

    Kornienko, Andrei

    2006-01-01

    The knowledge of dynamical characteristics of a flight vehicle is necessary for the control system design and realization of high fidelity flight simulators. The development of a flight mechanical model and determination of its basic components, as for example mass properties and the major aerodynamic terms, addresses a complex process involving various analytical, numerical and experimental techniques. The objective of this dissertation is a determination of the basic dynamical character...

  14. System and method for clock synchronization and position determination using entangled photon pairs

    Science.gov (United States)

    Shih, Yanhua (Inventor)

    2010-01-01

    A system and method for clock synchronization and position determination using entangled photon pairs is provided. The present invention relies on the measurement of the second order correlation function of entangled states. Photons from an entangled photon source travel one-way to the clocks to be synchronized. By analyzing photon registration time histories generated at each clock location, the entangled states allow for high accuracy clock synchronization as well as high accuracy position determination.

  15. Validated spectrofluorometric method for determination of gemfibrozil in self nanoemulsifying drug delivery systems (SNEDDS)

    OpenAIRE

    Sierra Villar, Ana María; Calpena Campmany, Ana Cristina; Halbaut, Lyda; Aróztegui Trenchs, Montserrat; Clares Naveros, Beatriz

    2013-01-01

    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 (r(2)>0.999) and low lim...

  16. The Development of a Low Cost, Modular Attitude Determination and Control System

    OpenAIRE

    Surka, Derek; Paluszek, Michael

    1997-01-01

    In an attempt to reduce the cost of future satellites, new technologies are being pursued to develop a modular attitude determination and control system that will provide three-axis control and cost less than ten percent of present systems. The low cost and modularity of this system make it especially attractive to a wide variety of small satellites. This paper will present the design and developmental status of this "plug and play" attitude control system. The general idea is to provide a co...

  17. Pulsatile microfluidics as an analytical tool for determining the dynamic characteristics of microfluidic systems

    DEFF Research Database (Denmark)

    Vedel, Søren; Olesen, Laurits Højgaard; Bruus, Henrik

    2010-01-01

    An understanding of all fluid dynamic time scales is needed to fully understand and hence exploit the capabilities of fluid flow in microfluidic systems. We propose the use of harmonically oscillating microfluidics as an analytical tool for the deduction of these time scales. Furthermore, we......-filled interconnected elastic microfluidic tubes containing a large, trapped air bubble and driven by a pulsatile pressure difference. We demonstrate good agreement between the system-level model and the experimental results, allowing us to determine the dynamic time scales of the system. However, the generic analysis...... can be applied to all microfluidic systems, both ac and dc....

  18. Satellite Positioning and Orbit Determination System SPODS:Theory and Test

    OpenAIRE

    WEI Ziqing; RUAN Rengui; Jia, Xiaolin; WU Xianbing; SONG Xiaoyong; MAO Yue; FENG Laiping; Zhu, Yongxing

    2016-01-01

    The Satellite Positioning and Orbit Determination System(SPODS)is a software package for GNSS positioning/orbit determination,developed by the Xi'an Research Institute of Surveying and Mapping.So far it has been able to treat GPS data and has the capability of high precision GPS positioning and orbit determination.The underlying theory and the performance test are briefly addressed.The test utilizes the GPS data collected from some 127IGS stations during days 4~10of 2009.The results show that...

  19. Pulsatile microfluidics as an analytical tool for determining the dynamic characteristics of microfluidic systems

    International Nuclear Information System (INIS)

    An understanding of all fluid dynamic time scales is needed to fully understand and hence exploit the capabilities of fluid flow in microfluidic systems. We propose the use of harmonically oscillating microfluidics as an analytical tool for the deduction of these time scales. Furthermore, we suggest the use of system-level equivalent circuit theory as an adequate theory of the behavior of the system. A novel pressure source capable of operation in the desired frequency range is presented for this generic analysis. As a proof of concept, we study the fairly complex system of water-filled interconnected elastic microfluidic tubes containing a large, trapped air bubble and driven by a pulsatile pressure difference. We demonstrate good agreement between the system-level model and the experimental results, allowing us to determine the dynamic time scales of the system. However, the generic analysis can be applied to all microfluidic systems, both ac and dc.

  20. A novel automated discontinuous venous blood monitoring system for ex vivo glucose determination in humans.

    Science.gov (United States)

    Schaller, R; Feichtner, F; Köhler, H; Bodenlenz, M; Plank, J; Wutte, A; Mader, J K; Ellmerer, M; Hellmich, R; Wedig, H; Hainisch, R; Pieber, T R; Schaupp, L

    2009-03-15

    Intensive insulin therapy reduces mortality and morbidity in critically ill patients but imposes great demands on medical staff who must take frequent blood samples for the determination of glucose levels. A solution to this resourcing problem would be provided by an automated blood monitoring system. The aim of the present clinical study was to evaluate such a system comprising an automatic blood sampling unit linked to a glucose biosensor. Our approach was to determine the correlation and system error of the sampling unit alone and of the combined system with respect to reference levels over 12h in humans. Two venous cannulae were inserted to connect the automatic and reference systems to the subjects. Blood samples were taken at 15 and 30 min intervals. The median Pearson coefficient of correlation between manually and automatically withdrawn blood samples was 0.982 for the sampling unit alone and 0.950 for the complete system. The biosensor had a linear range up to 20 mmoll(-1) and a 95% response time of Titration Error Grid analysis suggested an acceptable treatment in 99.56% of cases. Implementation of a "Keep Vein Open" saline infusion into the automated blood sampling system reduced blood withdrawal failures through occluded catheters fourfold. In summary, automated blood sampling from a peripheral vein coupled with automatic glucose determination is a promising alternative to frequent manual blood sampling. PMID:19135351

  1. 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.

  2. 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.

  3. ZOCT and chaotic oscillator applied to fault section determination in distribution system

    Science.gov (United States)

    Shang, Qiufeng; Zhou, Wenchang

    2006-11-01

    It's a new idea for using zero-sequence optical current transducer (ZOCT) to solve the measure problem of single-phase-to-ground fault section determination in distribution system. However the outputs of ZOCT are weak and mixed with noises, decreasing the detection sensitivity. Chaotic oscillator system is sensitive to certain signal and immune to noise, so the signal detection based on Duffing oscillator can improve the detection sensitivity and anti-interference capability. In this paper, combining Duffing oscillator with ZOCT, a new scheme of fault section determination is presented, with good sensitivity and reliability. The results of simulation and experiments proved this method is effective and feasible.

  4. Star Tracker Algorithms and a Low-Cost Attitude Determination and Control System for Space Missions

    OpenAIRE

    Delabie, Tjorven

    2016-01-01

    The attitude determination and control system determines and controls the orientation of the spacecraft. This system is crucial in the majority of space missions to e.g. point a camera to a star or direct an antenna to a ground station. Increasingly complex missions drive the need for higher accuracy, while the growing number of small spacecraft requires high robustness and low computational cost. This work focusses on the star tracker, a sensor that takes an image of the stars and compares i...

  5. 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.

  6. System and method for determining stator winding resistance in an AC motor using motor drives

    Energy Technology Data Exchange (ETDEWEB)

    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.

  7. Star trackers, star catalogs, and attitude determination - Probabilistic aspects of system design

    Science.gov (United States)

    Vedder, John D.

    1992-01-01

    Optimizing spacecraft attitude determination systems that use onboard star trackers requires analysis and evaluation of some probabilistic aspects of system design. This paper discusses methods of constructing or compiling optimum star catalogs, which are defined as uniform distributions on a sphere. Both local and global measures of uniformity on a sphere are defined. Application of these methods and measures to a specific problem is also discussed. In addition, Poisson models of star tracker acquisition probabilities are formulated to provide a useful analytical basis for designing and optimizing attitude determination systems. These analytical models and methods lead to rapid and realistic quantitative results, and should therefore facilitate making system performance trades. Use of such methods should also reduce the need for performing tedious computer simulations to obtain analogous results.

  8. Development of an Optical system for the determination of concentration of fine particulate material

    International Nuclear Information System (INIS)

    We have developed a new system of passive recollection of fine particulate material present in ambient air. Preliminary measurements under field conditions show the success of the new design with an increased collection efficiency. In addition, we have used a simple optical system as an alternative to the regular gravimetric technique for the determination of particle concentration. Laboratory tests of the optical method display good correlation with standard mass measurements. (Author)

  9. General Criteria for Determining Rotation or Oscillation in a Two-dimensional Axisymmetric System

    OpenAIRE

    Koyano, Yuki; Yoshinaga, Natsuhiko; Kitahata, Hiroyuki

    2014-01-01

    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 oscillato...

  10. 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. PMID:26156475

  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. Firm-Level Determinants of Board System Choice: Evidence from Russia

    OpenAIRE

    Iwasaki, Ichiro

    2013-01-01

    In this paper, using a unique data set of joint-stock companies, we empirically examine the determinants of the choice and size of the collective executive board, a core element of the multi-tier board system of Russian firms. Our empirical evidence strongly suggests that the need of company executives for a collective management system is a key driver for the formation of a collective executive board, while outside investors are generally indifferent toward its adoption as a means to strengt...

  13. Design of the Active Attitude Determination and Control System for the e-st@r cubesat

    OpenAIRE

    Stesina, Fabrizio; Corpino, Sabrina; Mozzillo, Raffaele; Obiols Rabasa, Gerard

    2012-01-01

    One of the most limiting factors which affects pico/nano satellites capabilities is the poor accuracy in attitude control. To improve mission performances of this class of satellites, the capability of controlling satellite's attitude shall be enhanced. The paper presents the design, development and verification of the Active Attitude Determination and Control System (A-ADCS) of the E-ST@R Cubesat developed at Politecnico di Torino. The heart of the system is an ARM9 microcontroller that mana...

  14. Lumbar Segmental Motion Properties In vivo Determined by a New Intraoperative Measurement System

    OpenAIRE

    Takano, Ko; Hasegawa, Kazuhiro; Kitahara, Ko; Hara, Toshiaki; Sato, Sakae; ENDO, Naoto

    2006-01-01

    In vivo quantitative evaluation of lumbar segmental stability has not been established yet. We developed a new measurement system to determine intraoperative lumbar stability. The purposes of this study were to measure in vivo segmental stability and to clarify the relationships between the preoperative radiographic findings and intraoperative measurement parameters. The system consisted of spinous process holders, a motion generator, load cell, optical displacement transducer, and computer. ...

  15. Determination of geomechanical parameters using a KBS system and application to an underground station

    OpenAIRE

    Miranda, Tiago F. S.; Correia, A. Gomes; Sousa, L. R.

    2005-01-01

    In this paper a KBS computational system, designated by GEOPAT, for the calculation of geomechanical parameters for modelling underground structures in rock and soil formations is presented. To congregate the specialists' knowledge in rock and soil domains, and in particular in the tunnel engineering, causal nets have been established for decision support. GEOPAT determines the parameters for rock and soil formations, as well as heterogeneous rock formations. The developed GEOPAT system was a...

  16. Determination of the modulation transfer function (MTF) of a screen-film system

    International Nuclear Information System (INIS)

    The assessment of image quality of a system depends on the task for which the system is intended Modulation transfer function (MTF) is used to describe relevant concepts often used in the analysis of the physical aspects of radiographic image quality. MTF particularly is used as one qf the parameters to determine the sharpness and has been used successfully to characterize the resolution properties of conventional analogue and digital X-ray imaging systems. It is also a basic medical imaging characteristic of the General Radiography X-ray system. This paper presents in brief the determination of MTF of a screen film system, which is most frequently used as an imaging component in diagnostic radiology. To measure MTF of a film screen system, the square wave response function method is used in this method, the square bar pattern with 15 groups of line-pair made of 0.05 mm lead, is used. The square bar pattern image will be changed to digitized data by using digitizer. Then it is analysed in order to get the characteristic curve and calibration curve. Data that are obtained from the graphs are interpolated to determine the MTF values. (Author)

  17. Ubiquitous Positioning: A Taxonomy for Location Determination on Mobile Navigation System

    Directory of Open Access Journals (Sweden)

    Wan Bejuri

    2011-03-01

    Full Text Available The location determination in obstructed area can be very challenging especially if Global PositioningSystem are blocked. Users will find it difficult to navigate directly on-site in such condition, especiallyindoor car park lot or obstructed environment. Sometimes, it needs to combine with other sensors andpositioning methods in order to determine the location with more intelligent, reliable and ubiquity. Byusing ubiquitous positioning in mobile navigation system, it is a promising ubiquitous location techniquein a mobile phone since as it is a familiar personal electronic device for many people. However, there isan increasing need for better development of proposed ubiquitous positioning systems. System developersare also lacking of good frameworks for understanding different options during building ubiquitouspositioning systems. This paper proposes taxonomy to address both of these problems. The proposedtaxonomy has been constructed from a literature study of papers and articles on positioning estimationthat can be used to determine location everywhere on mobile navigation system. For researchers thetaxonomy can also be used as an aid for scoping out future research in the area of ubiquitous positioning.

  18. Photogrammetry System and Method for Determining Relative Motion Between Two Bodies

    Science.gov (United States)

    Miller, Samuel A. (Inventor); Severance, Kurt (Inventor)

    2014-01-01

    A photogrammetry system and method provide for determining the relative position between two objects. The system utilizes one or more imaging devices, such as high speed cameras, that are mounted on a first body, and three or more photogrammetry targets of a known location on a second body. The system and method can be utilized with cameras having fish-eye, hyperbolic, omnidirectional, or other lenses. The system and method do not require overlapping fields-of-view if two or more cameras are utilized. The system and method derive relative orientation by equally weighting information from an arbitrary number of heterogeneous cameras, all with non-overlapping fields-of-view. Furthermore, the system can make the measurements with arbitrary wide-angle lenses on the cameras.

  19. Determination of the linear equations of position-sensing detectors for small motion measurement systems.

    Science.gov (United States)

    Liu, Chien-Sheng; Lin, Psang Dain

    2010-11-01

    Small motion measurement systems are widely used in industry measurement fields to measure small positional/angular motions. These systems usually consist of two parts: a measuring assembly and a reference assembly. The position-sensing detectors (PSDs) are embedded in either measuring assembly or reference assembly to sense the variations of laser light incidence points when there are any small positional/angular motions. To use these systems, it is necessary to determine the linear equations of PSD readings, which relate the six-degrees-of-freedom small positional/angular motions and PSD readings. The purpose of this paper is to derive these equations based on the paraxial raytracing method. Two measurement systems are used as illustrative examples to validate the proposed methodology. The methodology of this study will be useful for system design of PSD-based measurement systems and their applications. PMID:21045913

  20. Determination of the tube voltage from clinic mammographic system using two types of detectors

    Energy Technology Data Exchange (ETDEWEB)

    Barreira, Jacqueline S.; Vivolo, Vitor, E-mail: jacsales@usp.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2014-07-01

    The use of X rays for diagnostic radiology is very common and important to Medicine, including mammographic diagnosis focusing decreasing of the doses applied to the patients and preserving high quality of the diagnostic image. A quality control program of the irradiation systems it is necessary to control periodically the performance of the X-ray systems applied in that diagnosis in order to obtain the best results in that diagnosis. The verification of the beam characteristics is made by using standard dosimetric procedures which include the determination of the kilovoltage and the kerma rates for the different radiation qualities applied in the diagnosis. The Instruments Calibration Laboratory (LCI) of IPEN perform calibration in dosemeters used in radiation dosimetry (in diagnostic radiology) for many years and are improving their methodology to attend the actual demand of that equipment used in quality control of that X-radiation systems. The objective of that paper were the measurements of kVp and air kerma produced for one mammographic system of LCI, Model VMI - Graphmammo AF (Philips) using two different measurements systems from PTW (Diavolt) and Radcal (kVp meter) that procedure is just to determine the stability of that system that is used to perform diagnosis in mammography level. The results obtained with the two systems utilized shows good agreement. That measurement can be applied at a routine quality control program of that X-ray system. (author)

  1. Protolytic equilibria in homogeneous and heterogeneous systems of ketoconazole and its direct spectrophotometric determination in tablets

    Directory of Open Access Journals (Sweden)

    MIRJANA P. VOJIC

    2005-02-01

    Full Text Available The acid-base equilibria of a diprotic, slightly hydrosoluble base ketoconazole were studied in homogeneous and heterogeneous water systems. The determinations were performed at 25 ºC at a constant ionic strength of 0.1M(NaCl. The acidity constant Ka1 was determined by potentiometric (pKa1 3.20 and spectrophotometric (pKa1 3.26 methods. A pKa2 constant of 6.10 was obtained based on the equilibrium constants pKs0 4.84 and pKs1 –1.26, determined in a heterogeneous ketoconazole system. The obtained values of the constants served to calculate the solubility and the distribution of the equilibrium forms of ketoconazole as a function of pH. On the basis of the distribution of the equilibrium forms of ketoconazole, a spectrophotometric method for the determination of its content in commercial tablets was developed. The determinations were performed at 225 nm in 0.1 M HCl. The method is simple and rapid and enables the direct spectrophotometric determination of the content of ketoconazole without previous isolation.

  2. A computational model for determining the minimal cost expansion alternatives in transmission systems planning

    International Nuclear Information System (INIS)

    A computational model for determining an economical transmission expansion plan, based in the decomposition techniques is presented. The algorithm was used in the Brazilian South System and was able to find an optimal solution, with a low computational resource. Some expansions of this methodology are been investigated: the probabilistic one and the expansion with financier restriction. (C.G.C.). 4 refs, 7 figs

  3. 40 CFR 63.4165 - How do I determine the emission capture system efficiency?

    Science.gov (United States)

    2010-07-01

    ... section are met: (1) The capture system meets the criteria in Method 204 of appendix M to 40 CFR part 51... building enclosure in Method 204 of appendix M to 40 CFR part 51. (2) Use Method 204A or 204F of appendix M to 40 CFR part 51 to determine the mass fraction of TVH liquid input from each coating, thinner,...

  4. Methods to Use Surface Infiltration Tests in Permeable Pavement Systems to Determine Maintenance Frequency

    Science.gov (United States)

    Currently, there is limited guidance on selecting test sites to measure surface infiltration rates in permeable pavement systems to determine maintenance frequency. The ASTM method (ASTM C1701) for measuring infiltration rate of in-place pervious concrete suggest to either (1) p...

  5. A study and development of a system for the determination of porus plates permeability

    International Nuclear Information System (INIS)

    A device employed for the study of flux in porous media and another one employed for the determination of permeability of porous plate are presented in this work. Experimental data and calculation obtained from the above cited systems are also presented. (author)

  6. Automatic microdistillation flow-injection system for the spectrophotometric determination of fluoride.

    Science.gov (United States)

    Shimada, Katsuhisa; Shimoda, Tetsuro; Kokusen, Hisao; Nakano, Shigenori

    2005-03-31

    An automatic flow-injection (FI) system including on-line separation by microdistillation and spectrophotometric detection has been developed for the determination of trace amounts of fluoride. This ion was separated from sample matrix by distillation in the presence of sulfuric and phosphoric acids, and was subsequently determined with spectrophotometry based on the mixed-ligand complex of lanthanum(III)-fluoride-alizarin complexone. The proposed FI system has high sampling frequency (20 samplesh(-1)), small sample size (600 microl) and the dynamic range of 0.05-15 mgl(-1) with relative standard deviations of below 1.2%. Interfering ions such as aluminum(III) and iron(III) was effectively eliminated. The method was successfully applied to the determination of fluoride in industrial drainage after water treatment. PMID:18969965

  7. 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

    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...... 80) an unacceptable recovery was found (9%). The contact time needed for obtaining chemical equilibrium was tested in the ER-H system by performing five test with different duration (1, 2, 4, 7 and 19 days) using the low organic carbon soil. Seven days of contact time appeared sufficient for......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...

  8. Dual-channel filter photometer system for biocomponent content determination in diesel oil

    Science.gov (United States)

    Gołębiowski, Jacek; Prohuń, Tomasz

    2008-07-01

    Currently, infrared spectrometry is the most often used method of determination of the biocomponent content in diesel oil, but this is also an expensive and time-consuming process. In this study, a portable, low-cost dual-channel filter photometer system is presented which meets the requirements of the European standard for biocomponent concentration measurements in diesel fuel. The results obtained using this novel system are reported and compared to the measurements made using a standard infrared spectrometer for biodiesel concentration between 0% and 20% by weight. The advantages of the new system, such as its adaptability to the different environmental conditions of analysis, are also discussed.

  9. Dual-channel filter photometer system for biocomponent content determination in diesel oil

    International Nuclear Information System (INIS)

    Currently, infrared spectrometry is the most often used method of determination of the biocomponent content in diesel oil, but this is also an expensive and time-consuming process. In this study, a portable, low-cost dual-channel filter photometer system is presented which meets the requirements of the European standard for biocomponent concentration measurements in diesel fuel. The results obtained using this novel system are reported and compared to the measurements made using a standard infrared spectrometer for biodiesel concentration between 0% and 20% by weight. The advantages of the new system, such as its adaptability to the different environmental conditions of analysis, are also discussed

  10. Analytical method for internal dose determination caused by chronically radionuclides inhalation to respiration system

    International Nuclear Information System (INIS)

    Analytical method for internal dose determination caused by chronically radionuclides inhalation to respiratory system with the constant rate of radionuclide concentration inhaled has been developed. The dose calculation is solved solved analytically using distribution and accumulation of radionuklida model in respiratory system. A computer program was then made to calculate internal dose in respiratory system easily and quickly. Computer program is arranged using Borland C++ 4.5 language. The value of internal dose on time t after inhalation depend on the radionuclides, the half time ,radionuclides AMAD, radionuclides class, radiation type, energy absorbed by respiratory organ, organ mass, the radionuclides concentration inhaled, the inhalation period

  11. Experimental determination of phase equilibria in the Fe-Nb-V ternary system

    International Nuclear Information System (INIS)

    The phase equilibria in the Fe-Nb-V ternary system were investigated by means of optical microscopy, electron probe microanalysis and X-ray diffraction. Four isothermal sections in the Fe-Nb-V ternary system at 1000 deg. C, 1100 deg. C, 1200 deg. C and 1300 deg. C were firstly experimentally established. Present experimental results indicate that: (1) there is a large (Nb, V) continuous bcc solid solution; (2) there are the larger solubilities of V in the FeNb and Fe2Nb phases. The newly determined phase equilibria in this system will provide important support for the development of hydrogen storage materials and microalloyed steels.

  12. Phase diagram determination and thermodynamic modeling of the Cu-Mg-Si system

    OpenAIRE

    Zhao J; Zhou J.; Liu S.; Du Y.; Tang S.; Yang Y

    2016-01-01

    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 ((Cu0.8Si0.2)2(Mg0.88Cu0.12)). A thermodynamic modeling for the Cu-Mg-Si system was then conducted on the basis of the experimental data obtained...

  13. 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

  14. Experimental determination of phase equilibria in the Co–V–Mo ternary system

    International Nuclear Information System (INIS)

    Highlights: ► Four isothermal sections of the Co–V–Mo system were experimentally determined. ► The solubility of Mo in the σ-Co2V3 phase increases with an increase in temperature region from 800 to 1200 °C. ► A large region of (V, Mo) continuous bcc solid solution was determined. -- Abstract: The phase equilibria in the Co–V–Mo ternary system were investigated by means of optical microscopy, electron probe microanalyzer and X-ray diffraction. Four isothermal sections of the Co–V–Mo ternary system at 800, 1000, 1100 and 1200 °C were experimentally established, and no ternary compound was found in this system. Experimental results show that the solubility of Mo in the σ-Co2V3 phase increases with an increase in temperature region from 800 to 1200 °C. The newly determined phase equilibria in this system will provide important information for the development of Co-based alloys

  15. Real-time Imaging Orientation Determination System to Verify Imaging Polarization Navigation Algorithm.

    Science.gov (United States)

    Lu, Hao; Zhao, Kaichun; Wang, Xiaochu; You, Zheng; Huang, Kaoli

    2016-01-01

    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. PMID:26805851

  16. 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.

  17. A combined photocatalytic determination system for chemical oxygen demand with a highly oxidative reagent

    International Nuclear Information System (INIS)

    This study focuses on the proposal and validation of a combined photocatalytic (PC) system and a three-parameterized procedure for the determination of chemical oxygen demand (COD; PcCODcombined), with a highly oxidative reagent utilized as a photoelectron scavenger and signal indicator. The PcCODcombined was the functional combination of photon-efficient thin-layer photocatalytic oxidation, conventional bulk-phase photocatalytic oxidation and photocarrier-efficient high-activity photocatalytic reduction in one single photodigestion system, and consequently, this system possessed high photon-utilization efficiency, automatic stirring function and satisfactory determination characteristics. In comparison with the conventional one-parameterized procedure, the three-parameterized procedure introduces the blank and total photocatalytic reduction responses as two of the three significant analytical parameters. Under the optimized pH value of 3.0-4.5 and a rotating rate of 40 rpm, the representative KMnO4 species was used for the PcCODcombined system as the combined high-activity oxidant, and a narrow and reliable analytical linear range of 0-260 mg L-1 was achieved during the 10 min duration of the determinations. No observable interference of Cl- was found at concentration of the ion up to 2000 mg L-1. A real sample analysis indicated that the measured values for the PcCODcombined were all within a relative deviation below 5% of CODCr of the standard method, which further validates the practical feasibility of the proposed PcCODcombined system.

  18. A technical approach for determining the importance of information in computerized alarm systems

    Energy Technology Data Exchange (ETDEWEB)

    Fortney, D.S. [Lawrence Livermore National Lab., CA (United States); Lim, J.J. [Lim and Orzechowski Associates, Alamo, CA (United States)

    1994-06-10

    Computerized alarm and access control systems must be treated as special entities rather than as generic automated information systems. This distinction arises due to the real-time control and monitoring functions performed by these systems at classified facilities and the degree of centralization of a site`s safeguards system information in the associated databases. As an added requirement for these systems, DOE safeguards and security classification policy is to protect information whose dissemination has the potential for significantly increasing the probability of successful adversary action against the facility, or lowering adversary resources needed for a successful attack. Thus at issue is just how valuable would specific alarm system information be to an adversary with a higher order objective. We have developed and applied a technical approach for determining the importance of information contained in computerized alarm and access control systems. The methodology is based on vulnerability assessment rather than blanket classification rules. This method uses a system architecture diagram to guide the analysis and to develop adversary defeat methods for each node and link. These defeat methods are evaluated with respect to required adversary resources, technical difficulty, and detection capability. Then they are incorporated into site vulnerability assessments to determine the significance of alarm system information in the context of a facility attack. This methodology was successfully applied to the Argus alarm, access control, and assessment system developed at the Lawrence Livermore National Lab. Argus is software-driven, contains interrelated databases, shares host computers, and communicates with field processors and alarms through a common network. The evaluation results provided insights into the importance of alarm system information while the methodology itself provided a framework for addressing associated information protection issues.

  19. Optimum capacity determination of stand-alone hybrid generation system considering cost and reliability

    International Nuclear Information System (INIS)

    Highlights: ► This paper presents a methodology for the installation capacity optimization. ► Hybrid generation system is optimized by application of adaptive genetic algorithm. ► A cost investigation is made under various conditions and component characteristics. ► The optimization scheme is validated to meet the annual power load demand. -- Abstract: The aim of this work is to present an optimization methodology for the installation capacity of a stand-alone hybrid generation system, taking into consideration the cost and reliability. Firstly, on the basis of derived steady state models of a wind generator (WG), a photovoltaic array (PV), a battery and an inverter, the hybrid generation system is modeled for the purpose of capacity optimization. Secondly, the power system is analyzed for determining both the system structure and the operation control strategy. Thirdly, according to hourly weather database of wind speed, temperature and solar irradiation, annual power generation capacity is estimated for the system match design in order that an annual power load demand can be met. The capacity determination of a hybrid generation system becomes complicated as a result of the uncertainty in the renewable energy together with load demand and the nonlinearity of system components. Aimed at the power system reliability and the cost minimization, the capacity of a hybrid generation system is optimized by application of an adaptive genetic algorithm (AGA) to individual power generation units. A total cost investigation is made under various conditions, such as wind generator power curves, battery discharge depth and the loss of load probability (LOLP). At the end of this work, the capacity of a hybrid generation system is optimized at two installation sites, namely the offshore Orchid Island and Wuchi in Taiwan. The optimization scheme is validated to optimize power capacities of a photovoltaic array, a battery and a wind turbine generator with a relative

  20. Statistical Determination of the Gating Windows for Respiratory-Gated Radiotherapy Using a Visible Guiding System.

    Science.gov (United States)

    Oh, Se An; Yea, Ji Woon; Kim, Sung Kyu

    2016-01-01

    Respiratory-gated radiation therapy (RGRT) is used to minimize the radiation dose to normal tissue in lung-cancer patients. Although determining the gating window in the respiratory phase of patients is important in RGRT, it is not easy. Our aim was to determine the optimal gating window when using a visible guiding system for RGRT. Between April and October 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 guided breathing in RGRT. When we compared breathing signals before and after the breathing training, 19 of the 23 patients showed statistically significant differences (p < 0.05). The standard deviation of the respiration signals after breathing training was lowest for phases of 30%-70%. The results showed that the optimal gating window in RGRT is 40% (30%-70%) with respect to repeatability for breathing after respiration training with the visible guiding system. RGRT was performed with the RPM system to confirm the usefulness of the visible guiding system. The RPM system and our visible guiding system improve the respiratory regularity, which in turn should improve the accuracy and efficiency of RGRT. PMID:27228097

  1. Numerical determination of the transmissibility characteristics of a squeeze film damped forced vibration system

    Science.gov (United States)

    Sutton, M. A.; Davis, P. K.

    1976-01-01

    Numerical solutions of the governing equations of motion of a liquid squeeze film damped forced vibration system were carried out to examine the feasibility of using a liquid squeeze film to cushion and protect large structures, such as buildings, located in areas of high seismic activity. The mathematical model used was that for a single degree of freedom squeeze film damped spring mass system. The input disturbance was simulated by curve fitting actual seismic data with an eleventh order Lagranging polynomial technique. Only the normal component of the seismic input was considered. The nonlinear, nonhomogeneous governing differential equation of motion was solved numerically to determine the transmissibility over a wide range of physical parameters using a fourth-order Runge-Kutta technique. It is determined that a liquid squeeze film used as a damping agent in a spring-mass system can significantly reduce the response amplitude for a seismic input disturbance.

  2. Radioimmunoassay determination of urinary prostaglandins in patients with progressive systemic sclerosis

    International Nuclear Information System (INIS)

    The results of urinary determinations of E-2 prostaglandines by radioimmunoassay (RIA) in 24-hour urine are presented for three groups: progressive systemic sclerotic patients with normotension and with elevated or normal APR, progressive systemic sclerotic patients with hypertension and with normal or low APR, control group of normal subjects. In a recent report of progressive systemic sclerosis in patients we demonstrated changes in the urine concentratrion of APR levels, sodium excretion and in total blood volume. Based on these findings we felt the need to perform quantifications of E-2 prostaglandines (PGE-2) in 24-hour recently taken urine samples stored at 700 and measure the sodium amounts excreted in the urine. We concluded that urinary determination of E-2 prostaglandines was the most suitable for our study as it allowed the establishment of relationships between APR, aldosterone and metabolic sodium balance. (author)

  3. A radioimmunological analytical system for thyroid peroxidase determination in biological tissue extracts

    International Nuclear Information System (INIS)

    An analytical system for radioimmunological determination of human thyroid peroxidase (TPO) has been developed for the first time. This system includes lyophilised preparations of human autoantibodies to TPO, radioiodinated TPO, standards prepared with the use of pure TPO and immobilized protein A as a solid phase precipitating agent. The specific binding of [125I] TPO in the system accounts for 35-40%, the non-specific binding of the radioactive label do not exceed 5%. TPO is accurately determined in a concentration range 8 to 1000 microgram/l, and the total analysis takes 3 h. The procedure and reagents developed can be applied in a technology of TPO isolation and purification from thyroid tissue extracts, that is intended for immuno analytical kits production

  4. Comparative effect of physicomechanical and biomolecular cues on zone-specific chondrogenic differentiation of mesenchymal stem cells.

    Science.gov (United States)

    Moeinzadeh, Seyedsina; Pajoum Shariati, Seyed Ramin; Jabbari, Esmaiel

    2016-06-01

    Current tissue engineering approaches to regeneration of articular cartilage rarely restore the tissue to its normal state because the generated tissue lacks the intricate zonal organization of the native cartilage. Zonal regeneration of articular cartilage is hampered by the lack of knowledge for the relation between physical, mechanical, and biomolecular cues and zone-specific chondrogenic differentiation of progenitor cells. This work investigated in 3D the effect of TGF-β1, zone-specific growth factors, optimum matrix stiffness, and adding nanofibers on the expression of chondrogenic markers specific to the superficial, middle, and calcified zones of articular cartilage by the differentiating human mesenchymal stem cells (hMSCs). Growth factors included BMP-7, IGF-1, and hydroxyapatite (HA) for the superficial, middle, and calcified zones, respectively; optimum matrix stiffness was 80 kPa, 2.1 MPa, and 320 MPa; and nanofibers were aligned horizontal, random, and perpendicular to the gel surface. hMSCs with zone-specific cell densities were encapsulated in engineered hydrogels and cultured with or without TGF-β1, zone-specific growth factor, optimum matrix modulus, and fiber addition and cultured in basic chondrogenic medium. The expression of encapsulated cells was measured by mRNA, protein, and biochemical analysis. Results indicated that zone-specific matrix stiffness had a dominating effect on chondrogenic differentiation of hMSCs to the superficial and calcified zone phenotypes. Addition of aligned nanofibers parallel to the direction of gel surface significantly enhanced expression of Col II in the superficial zone chondrogenic differentiation of hMSCs. Conversely, biomolecular factor IGF-1 in combination with TGF-β1 had a dominating effect on the middle zone chondrogenic differentiation of hMSCs. Results of this work could potentially lead to the development of multilayer grafts mimicking the zonal organization of articular cartilage. PMID:27038568

  5. Experimental determination and thermodynamic calculation of the phase equilibria in the Co-Mn-Ta system

    International Nuclear Information System (INIS)

    The phase equilibria in the Co-rich corner of the Co-Mn-Ta system were investigated by means of optical microscopy, electron probe microanalysis and X-ray diffraction. Six isothermal sections in the Co-rich corner of the Co-Mn-Ta ternary system at 1300 C, 1200 C, 1100 C, 1000 C, 900 C, 800 C were experimentally determined. On the basis of previous and present experimental data of the phase equilibria, the thermodynamic assessments of the Mn-Ta binary and Co-Mn-Ta ternary systems were carried out by using CALPHAD. The thermodynamic parameters of the Mn-Ta binary and the Co-Mn-Ta ternary systems have been optimized for reproducing the experimental results in each system. An agreement between the calculated results and experimental data is obtained.

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

    DEFF Research Database (Denmark)

    Zabic, Martina

    function. The thesis provides a thorough review of the different GNSS-based trials and experiments conducted within recent years to assess the performance and possibilities of GNSSbased charging systems. In 2007–2009, a GNSS-based road charging experiment was conducted in Copenhagen as part of this...... research in cooperation with Siemens to assess the performance and technical challenges of GNSS-based road charging systems based on state of the art road charging technology. This thesis presents the experiment conducted and provides an assessment of the vehicle location determination function within GNSS......-based road charging systems. Previous trials and performance assessments of GNSS-based road charging systems have generally focused on the possibilities of the charging systems rather than on the impossibilities. Often it has not been clearly described which errors and shortages existed in the collected data...

  7. 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.

  8. Titrimetric determination of Zr, Hf, Sn, Ta and rare earths in binary oxide systems

    International Nuclear Information System (INIS)

    Proximate method of titrimetric determination of oxides of Zr(4), Hf(4), Sn(4), Ta(5) and rare earths (La, Lu, Nd, Eu, Yb, Y) in binary systems (BS) with high accuracy was developed. A study was made on conditions of decomposition and dissolution of BS by means of their treatment by the mixture of solutions of concentrated sulfuric acid and ammonium sulfate during 2h boiling eith successive complexonometric determination of their components by direct EDTA titration in the presence of xylenol orange. The relative standard deviation when titrating 0.3-9.7mg oxides in BS does not exceed 0.02

  9. Determination of critical micelle concentrations in micellar and reversed micellar systems by positron annihilation techniques

    International Nuclear Information System (INIS)

    The applicability of the positron annihilation technique is discussed as a simple method for the accurate determination of the critical micelle concentration (cmc). The results of a preliminary study of positron interactions in solutions with various amounts of surfactants present are reported. The six different micellar systems studied were dodecylammonium propionate in benzene, cyclohexane, and n-hexane; sodium di(2-ethylhexyl)sulfosuccinate in benzene; sodium decylsulfate and decyltrimethylammonium bromide in water. The tabulated results indicated that this technique was applicable to the determination of cmc's in both aqueous and nonaqueous solutions

  10. Microbial trench-based optofluidic system for reagentless determination of phenolic compounds.

    Science.gov (United States)

    Sanahuja, David; Giménez-Gómez, Pablo; Vigués, Núria; Ackermann, Tobias Nils; Guerrero-Navarro, Alfons Eduard; Pujol-Vila, Ferran; Sacristán, Jordi; Santamaria, Nidia; Sánchez-Contreras, María; Díaz-González, María; Mas, Jordi; Muñoz-Berbel, Xavier

    2015-04-01

    Phenolic compounds are one of the main contaminants of soil and water due to their toxicity and persistence in the natural environment. Their presence is commonly determined with bulky and expensive instrumentation (e.g. chromatography systems), requiring sample collection and transport to the laboratory. Sample transport delays data acquisition, postponing potential actions to prevent environmental catastrophes. This article presents a portable, miniaturized, robust and low-cost microbial trench-based optofluidic system for reagentless determination of phenols in water. The optofluidic system is composed of a poly(methyl methacrylate) structure, incorporating polymeric optical elements and miniaturized discrete auxiliary components for optical transduction. An electronic circuit, adapted from a lock-in amplifier, is used for system control and interfering ambient light subtraction. In the trench, genetically modified bacteria are stably entrapped in an alginate hydrogel for quantitative determination of model phenol catechol. Alginate is also acting as a diffusion barrier for compounds present in the sample. Additionally, the superior refractive index of the gel (compared to water) confines the light in the lower level of the chip. Hence, the optical readout of the device is only altered by changes in the trench. Catechol molecules (colorless) in the sample diffuse through the alginate matrix and reach bacteria, which degrade them to a colored compound. The absorbance increase at 450 nm reports the presence of catechol simply, quickly (~10 min) and quantitatively without addition of chemical reagents. This miniaturized, portable and robust optofluidic system opens the possibility for quick and reliable determination of environmental contamination in situ, thus mitigating the effects of accidental spills. PMID:25669844

  11. Detecting and Quantifying Biomolecular Interactions of a Dendritic Polyglycerol Sulfate Nanoparticle Using Fluorescence Lifetime Measurements

    Directory of Open Access Journals (Sweden)

    Alexander Boreham

    2015-12-01

    Full Text Available Interactions of nanoparticles with biomaterials determine the biological activity that is key for the physiological response. Dendritic polyglycerol sulfates (dPGS were found recently to act as an inhibitor of inflammation by blocking selectins. Systemic application of dPGS would present this nanoparticle to various biological molecules that rapidly adsorb to the nanoparticle surface or lead to adsorption of the nanoparticle to cellular structures such as lipid membranes. In the past, fluorescence lifetime measurements of fluorescently tagged nanoparticles at a molecular and cellular/tissue level have been proven to reveal valuable information on the local nanoparticle environment via characteristic fluorescent lifetime signatures of the nanoparticle bound dye. Here, we established fluorescence lifetime measurements as a tool to determine the binding affinity to fluorescently tagged dPGS (dPGS-ICC; ICC: indocarbocyanine. The binding to a cell adhesion molecule (L-selectin and a human complement protein (C1q to dPGS-ICC was evaluated by the concentration dependent change in the unique fluorescence lifetime signature of dPGS-ICC. The apparent binding affinity was found to be in the nanomolar range for both proteins (L-selectin: 87 ± 4 nM and C1q: 42 ± 12 nM. Furthermore, the effect of human serum on the unique fluorescence lifetime signature of dPGS-ICC was measured and found to be different from the interactions with the two proteins and lipid membranes. A comparison between the unique lifetime signatures of dPGS-ICC in different biological environments shows that fluorescence lifetime measurements of unique dPGS-ICC fluorescence lifetime signatures are a versatile tool to probe the microenvironment of dPGS in cells and tissue.

  12. LESPRO - an expert system for the decision support in determination and suggestion of protective measures

    International Nuclear Information System (INIS)

    A prototype expert system for advising emergency procedures for nuclear regulatory authority has been developed. The expert system ESPRO is known as goal oriented rule-based knowledge system. The system is based on emergency procedures developed in VUJE Trnava, Inc. for use by the Emergency Response Centre (ERC) of the Slovak Nuclear Regulatory Authority (NRA). The operation interpretation module uses the knowledge base of emergency procedures for the evaluation of source term and determination and suggestion of protective measures which is represented in the form of a Petri net model. Its verification and validation was done on the basis of the results of two exercises: joint exercise of ERC staff with Slovak Army Headquarters and full scale Mochovce NPP emergency exercise with use of the Mochovce NPP simulator. (author)

  13. Asteroseismic Determination of Obliquities of the Exoplanet Systems Kepler-50 and Kepler-65

    DEFF Research Database (Denmark)

    Chaplin, W. J.; Sanchis-Ojeda, R.; Campante, T. L.;

    2013-01-01

    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 1s 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. © 2013. The American Astronomical Society. All rights reserved.....

  14. Qualitative and quantitative methods to determine miscibility in amorphous drug-polymer systems.

    Science.gov (United States)

    Meng, Fan; Dave, Vivek; Chauhan, Harsh

    2015-09-18

    Amorphous drug-polymer systems or amorphous solid dispersions are commonly used in pharmaceutical industry to enhance the solubility of compounds with poor aqueous solubility. The degree of miscibility between drug and polymer is important both for solubility enhancement as well as for the formation of a physically stable amorphous system. Calculation of solubility parameters, Computational data mining, Tg measurements by DSC and Raman mapping are established traditional methods used to qualitatively detect the drug-polymer miscibility. Calculation of Flory-Huggins interaction parameter, computational analysis of X-Ray Diffraction (XRD) data, solid state Nuclear Magnetic Resonance (NMR) spectroscopy and Atomic Forced Microscopy (AFM) have been recently developed to quantitatively determine the miscibility in amorphous drug-polymer systems. This brief review introduces and compiles these qualitative and quantitative methods employed in the evaluation of drug-polymer miscibility. Combination of these techniques can provide deeper insights into the true miscibility of the drug-polymer systems. PMID:26006307

  15. 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.

  16. Catalytic spectrophotometric determination of cerium by ion exchange separation coupled to a flow injection system

    International Nuclear Information System (INIS)

    A flow injection method is described intended for the determination of cerium based on its catalytic effect on the oxidation of gallocyanine by peroxydisulfate in acidic media. The proposed flow injection manifold incorporates a ion exchange separation system in the carrier stream. The decolorisation of gallocyanine due to its oxidation was used to monitor the reaction by spectrophotometry at 524 nm. The variables which affected the reaction rate were fully investigated. By this method cerium(4) can be determined in the range of 0.30-10.0 μg with a limit of detection of 0.25 μg. The relative standard deviation for ten replicate determinations of 1.0 μg of cerium(4) was 1.8 %

  17. REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.

    Science.gov (United States)

    Moritsugu, Kei; Smith, Jeremy C

    2008-08-01

    Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all alpha), plastocyanin (all beta), and dihydrofolate reductase (alpha/beta) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is presented, and low-temperature coarse-grained (CG) REACH MD simulations of the three proteins are compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the CGMD. Model functions for the CG interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the use of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations. PMID:18469078

  18. 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...

  19. 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.

  20. Determination of protein-ligand binding affinity by NMR: observations from serum albumin model systems.

    Science.gov (United States)

    Fielding, Lee; Rutherford, Samantha; Fletcher, Dan

    2005-06-01

    The usefulness of bovine serum albumin (BSA) as a model protein for testing NMR methods for the study of protein-ligand interactions is discussed. Isothermal titration calorimetry established the binding affinity and stoichiometry of the specific binding site for L-tryptophan, D-tryptophan, naproxen, ibuprofen, salicylic acid and warfarin. The binding affinities of the same ligands determined by NMR methods are universally weaker (larger KD). This is because the NMR methods are susceptible to interference from additional non-specific binding. The L-tryptophan-BSA and naproxen-BSA systems were the best behaved model systems. PMID:15816062

  1. 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

    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...... with the spectrophotometric method ( CV = 6.3%). These results indicate that the FACSCount AF System is a valuable tool for precise and accurate assessment of sperm concentration in boar semen and that use of this system may lead to production of more uniform insemination doses containing a specific number of sperm per dose....

  2. 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.

  3. An Effective Numerical Procedure to Determine Saddle-Type Unstable Invariant Limit Sets in Nonlinear Systems

    International Nuclear Information System (INIS)

    A new technique that can efficiently approximate the attracting set of a nonlinear dynamical system is proposed under the framework of point mapping with the cell reference method. With the aid of the approximated attracting set, the difficulties encountered by the PIM-triple method and bisection procedure in finding trajectories on the stable manifolds of chaotic saddles in basins of attraction and on basin boundaries can be overcome well. On the basis of this development, an effective method to determine saddle-type invariant limit sets of nonlinear dynamical systems can be devised. Examples are presented for the purposes of illustration and to demonstrate the capabilities of the proposed method. (general)

  4. Organization of information protection in the information system of determining the toxicity focus of biological objects

    OpenAIRE

    Руженцев, Віктор Ігоревич; Порван, Андрій Павлович; Пащенко, Марія Анатоліївна

    2016-01-01

    It is proposed an approach to the organization of information protection in the information system of determining the toxicity focus of aquatic biological objects to prevent unauthorized access to data. As the most efficient algorithm for the information protection has been elected a symmetric block encryption algorithm. The use of this algorithm is enabled to achieve the necessary and sufficient performance of operations of encryption and decryption of data monitoring of water bodies on diff...

  5. Determination the Appropriateness of Tokat Kazova Lands to Peach Cultivation Using Geographic Information System

    OpenAIRE

    R. Gercekcioglu; T. Susam; T. Oztekin

    2008-01-01

    The aims of this study are to determine the appropriate peach orchard locations among Tokat Kazova lands and to classify the lands according to the suitability for peach cultivation by means of Geographic Information System (GIS). The distances and elevation differences of possible orchard locations to/from the available water resources, soil profile depth, soil profile texture, frost risk, land aspect, and land slope were considered as criterions to classify the lands of Tokat Kazova to dete...

  6. Performance of DMPS/C System in Determining Aerosol Particle Size Distribution

    International Nuclear Information System (INIS)

    An evaluation of performance of DMPS/C system TSI-3932 in determining aerosol particle size has been carried out. The evaluation consist of validity of experimentally transfer function, instrument resolution, and test of measurement accuracy and precision for monodisperse and polydisperse aerosol size distribution. Evaluation of measurement accuracy gave a deviation of 0.74 %, and evaluation of measurement precision gave variation coefficient of 0,50 % and 1.63 % for monodisperse aerosol and polydisperse aerosol respectively

  7. Determining staffing requirements of non-stationary queueing systems based on the efficient frontier

    OpenAIRE

    Rosinski, Tobias

    2014-01-01

    Existing methods for the modelling and staffing of non-stationary queuing systems enable controlling the trade-off between costs and speed. However, the speed of the service is only one aspect of operational performance that affects customer satisfaction. The quality of the service provided by the servers, which may be as or even more important than the waiting time for the customer, cannot be considered yet. This research proposes to determine the time-dependent required number of servers ba...

  8. Accurate Determination of Nonlinear Refractive Index for Some Binary Glass Systems

    OpenAIRE

    ElSayed Moustafa

    2011-01-01

    Problem statement: This study investigates the relation between the nonlinear optical susceptibility (χ(3)) and the ratio (α1/αo-2), then the nonlinear index determination for some binary glass systems. Recently suitable relationship between the oxidation polarizability and the nonlinear optical properties was established for simple oxides glasses. So in this study more attention and investigation is paid to the trend of that relation quantitatively as possible. Approach: The i...

  9. Determination of Ciprofloxacin by Flow Injection Analysis Based on Chemiluminescence System

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A novel flow injection chemiluminescence (CL) method for the determination of ciprofloxacin (CPLX) was reported. The proposed method is based on luminescence produced by KMnO4-Na2S2O4-Tb3+-CPLX chemiluminescence (CL) system. The effects of some critical experimental conditions were discussed and the optimization of working condithe recoveries of real sample analyses were in the range from 110 ± 4 to 104 ± 4.

  10. 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.

  11. Determinants of fruit and vegetable consumption in Malaysia: an ordinal system approach

    OpenAIRE

    Yen, Steven T.; ANDREW K. G. TAN; Nayga, Rodolfo M. Jr.

    2011-01-01

    We examine the socio-demographic determinants of fruit and vegetable consumption using household survey data from Malaysia. A bivariate ordered probability model is developed by the copula approach. Results for a system of fruit and vegetable servings per week indicate that education, age, ethnicity, income, location of residence, smoking status and health conditions are significant predictors of fruit and vegetable consumption in Malaysia. Policy implications are suggested.

  12. Innovation Approach Based Sensor FDI in LEO Satellite Attitude Determination and Control System

    OpenAIRE

    Hajiyev, Chingiz

    2009-01-01

    Fault detection and isolation algorithms for LEO satellite attitude determination and control system using an approach for checking the statistical characteristics of EKF innovation sequence are proposed. The fault detection algorithm is based on statistic for the mathematical expectation of the spectral norm of the normalized innovation matrix of the EKF. This approach permits simultaneous real-time checking of the mathematical expectation and the variance of the innovation sequence and does...

  13. Evaluation of Biochip System in Determining Isoniazid and Rifampicin Resistances of Mycobacterium Tuberculosis in Sputum Samples

    OpenAIRE

    Lu, Wei; Chen, Cheng; Shao, Yan; Shi, Jinyan; Zhong, Chongqiao; Yang, Dandan; Song, Honghuan; Li, Guoli; Ding, Xiaoyan; Peng, Hong; Zhu, Linyang; Zhou, Yang; Zhu, Limei

    2012-01-01

    Objective To evaluate a biochip system in determining isoniazid and rifampicin resistances of Mycobacterium tuberculosis in sputum samples in a Chinese population. Methods We assembled 907 sputum smeared positive specimens of tuberculosis patients in total. Each sample would be separated into two parts for culture and biochip assay simultaneously. And those cultured positive and having full drug resistance results would be used as reference. The McNemar χ2 test was adopted for evaluating the ...

  14. XX/XY system of sex determination in the geophilomorph centipede Strigamia maritima

    Czech Academy of Sciences Publication Activity Database

    Green, J. E.; Dalíková, Martina; Sahara, K.; Marec, František; Akam, M.

    2016-01-01

    Roč. 11, č. 2 (2016), e0150292. E-ISSN 1932-6203 R&D Projects: GA AV ČR IAA600960925; GA ČR(CZ) GA14-22765S Institutional support: RVO:60077344 Keywords : sex determination * Strigamia maritima * XX/XY system Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 3.234, year: 2014 http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150292

  15. Information Systems Implementations : Models to Determine what Constitutes Success and Failure

    OpenAIRE

    Gunson, John; De Blasis, Jean-Paul; Esteves, José; Pastor, Joan

    2004-01-01

    This paper proposes Information System (IS) Implementation success criteria according to stakeholder viewpoints using Enterprise Applications Implementations as an example. Besides models for each type of stakeholder, a bi-polar model for gauging overall success of the project is proposed. A body of research exists which identifies Critical Success Factors and lately the relationship between these factors. In this paper we examine from a different angle the measures and determination of proje...

  16. [Functionality determinants of the integrated systems dedicated to health care institutions].

    Science.gov (United States)

    Sokołowski, Adam; Sroka, Mariusz

    2013-01-01

    The Authors of the hereby dissertation aimed at presenting the functionality concept of the integrated e-service platform dedicated to health care institutions. In the form of a problem repository the research results allowing the identification of the functionality determinants were presented. Finally, the study presents the system's structure as well as analyzing the needs for e-services in terms of society and their usefulness evaluated by branch experts. PMID:23905430

  17. 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.

  18. Analytic method of determination of the external design parameters in the microclimate systems of buildings

    Directory of Open Access Journals (Sweden)

    A.G. Sotnikov

    2013-03-01

    Full Text Available It is known that the external design parameters are quite important for designing heating, ventilation and air conditioning systems, because they determine design discharge of the building: cold (in summer and heat (in winter. Thus they substantially influence the capital and maintenance expenditure. Until recently in many countries the external design parameters are determined quite equally, exactly by arbitrarily given provision (probability of non-exceedance. Such way of determination of the external design parameters is the one in heating facilities and ventilating equipment that does not have any system-reasonable analytic methodology.The author of this paper, using the number of researches, suggests the appropriate method, referring to outside design temperature in the frost-free season. At a later date there will be proposed another methods for design moisture content – in summer and design temperature – in winter.Analytic dependences, that come from the study, take into account all the complex of characteristics: system, technological, climatological, hygienic, static, dynamic and also probabilistic. In particular it is proved, that rather essential parameter, that generally is not taken in account in computation, is outside air consumption in the compound with recirculated air. Therefore this method requires sufficient skills of the specialist, who must be well acquainted with related fields of knowledge, technics, appropriate terminology. The new method although requires the following discussion and probable improvement, but it allows determining the external design parameters more reasonable and less complicated. If it finds a broad response, it will be recommended for design standard of microclimate systems in different countries.

  19. Dynamic karyotype evolution and unique sex determination systems in Leptidea wood white butterflies

    OpenAIRE

    VOLENÍKOVÁ, Anna

    2015-01-01

    Chromosomal rearrangements such as fusions and fissions play an important role in promoting and maintaining speciation. To study these phenomena, genome architecture of three cryptic species of Leptidea wood white butterflies was investigated by means of standard and molecular cytogenetics. High variability in chromosome number and localization of cytogenetic markers was revealed, suggesting dynamic karyotype evolution in these species. Moreover, unique sex-determination system with 3-4 W chr...

  20. Determination of the critical micelle concentration in simulations of surfactant systems

    Science.gov (United States)

    Santos, Andrew P.; Panagiotopoulos, Athanassios Z.

    2016-01-01

    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).

  1. 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

  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. 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

  4. 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

  5. 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).

  6. 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.

  7. 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.

  8. Actinide 5f systems: experimental determination of the magnetic response function

    International Nuclear Information System (INIS)

    Understanding of metallic actinide systems is in confusion. Searches for crystal-field levels with neutron spectroscopy have, for the most part, been unsuccessful, despite the acknowledged importance of the 5f electrons in determining the magnetic behavior. In systems such as UAl2, USn3 and UN a broad response function, S(Q vector,ω), reminiscent of that found in intermediate valent compounds, exists. Neutron inelastic scattering experiments on single crystals have shown the small influence of the crystal field. Instead we find an unusual response function dominated by the longitudinal susceptibility chi/sup zz/(Q vector,,ω) such that transverse excitations - conventional spin waves - do not exist at low energies. As yet a detailed theoretical interpretation of the measurements does not exist. Indeed, the small, although not necessarily negligible, role of the crystal field presents conceptual difficulties if we anticipate behavior analogous to that found in many lanthanide 4f systems. Some alternate approaches are discussed

  9. A determination of degradation capability of RSG-GAS piping secondary cooling system

    International Nuclear Information System (INIS)

    A research of degradation capabilities of RSG-GAS secondary cooling piping system has been done in G.A. Siwabessy Multy Purpose Reactor Serpong. The research involved hardness test and thickness inspection of the pipe wall. The results of the research are 139 BHN and 1,085 mm for minimum hardness and minimum thickness of the pipe wall respectively. Booth of these data are used to determine the current maximum stress of the pipe. The comparison of the current stress and the design is magnitude of degradation capability. Since the degradation capability of the RSG-GAS secondary cooling piping system has been known, the maintenance management system could be established and reactor operation which is safe and reliable can be maintained. (author)

  10. Grid Inertial Response-Based Probabilistic Determination of Energy Storage System Capacity Under High Solar Penetration

    International Nuclear Information System (INIS)

    It is well-known that responsive battery energy storage systems (BESSs) are an effective means to improve the grid inertial response to various disturbances including the variability of the renewable generation. One of the major issues associated with its implementation is the difficulty in determining the required BESS capacity mainly due to the large amount of inherent uncertainties that cannot be accounted for deterministically. In this study, a probabilistic approach is proposed to properly size the BESS from the perspective of the system inertial response, as an application of probabilistic risk assessment (PRA). The proposed approach enables a risk-informed decision-making process regarding (1) the acceptable level of solar penetration in a given system and (2) the desired BESS capacity (and minimum cost) to achieve an acceptable grid inertial response with a certain confidence level

  11. Can one determine cosmological parameters from multi-plane strong lens systems?

    CERN Document Server

    Schneider, Peter

    2014-01-01

    Strong gravitational lensing of sources with different redshifts has been used to determine cosmological distance ratios, which in turn depend on the expansion history. Hence, such systems are viewed as potential tools for constraining cosmological parameters. Here we show that in lens systems with two distinct source redshifts, of which the nearest one contributes to the light deflection towards the more distant one, there exists an invariance transformation which leaves all strong lensing observables unchanged (except the product of time delay and Hubble constant), generalizing the well-known mass-sheet transformation in single plane lens systems. The transformation preserves the relative distribution of mass and light, so that a `mass-follows-light' assumption does not fix the MST. All time delays (from sources on both planes) scale with the same factor -- time-delay ratios are therefore invariant under the MST. Changing cosmological parameters, and thus distance ratios, is essentially equivalent to such a...

  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

    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....... 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......'' labels of a dataset. We make available a reproducible research package so that others can perform the same experiments with other MIR systems....

  13. DETERMINATION OF COLLECTION EFFICIENCY OF ATMOSPHERIC IONS BY THE SYSTEMS OF PARALLEL CONDUCTIVE PLATES

    Directory of Open Access Journals (Sweden)

    Floran Vila

    2013-03-01

    Full Text Available We present a theory that describes the scenarios of equations of motion of clustered air ions entering into specific systems. The system analyzed here is composed by two or three conductive parallel plates. In the first case (system of two parallel plates one plate collects air ions which enter into the area between these plates. In the second case (system of three parallel plates the collector plate is the middle one.Air ions usually are classified into several categories according to their electrical mobility (size. The main categories are: cluster ions (mobility 0.5-3.2 cm2/V.s, intermediate ions (mobility 0.034-0.5 cm2/V.s, and large ions (mobility 0.0042-0.034 cm2/V.s.This theory has an important application on ion counter operations. Usually the apparatus measures the concentrations of only cluster air ions (mobility > 0.5 cm2/V.s. Air ions are deflected by the electric field established by a potential difference of polarized plates. Air ion concentrations are derived from measurement of electrical current caused in the system.Based on this theory, we can determine analytically the efficiency of the collection of air ions of different electrical mobility by above mentioned systems.

  14. A new method to determine reflex latency induced by high rate stimulation of the nervous system

    Directory of Open Access Journals (Sweden)

    Ilhan Karacan

    2014-07-01

    Full Text Available High rate stimulations of the neuromuscular system, such as continuous whole body vibration, tonic vibration reflex and high frequency electrical stimulation, are used in the physiological research with an increasing interest. In these studies, the neuronal circuitries underlying the reflex responses remain unclear due to the problem of determining the exact reflex latencies. We present a novel “cumulated average method” to determine the reflex latency during high rate stimulation of the nervous system which was proven to be significantly more accurate than the classical method. The classical method, cumulant density analysis, reveals the relationship between the two synchronously recorded signals as a function of the lag between the signals. The comparison of new method with the classical technique and their relative accuracy was tested using a computer simulation. In the simulated signals the EMG response latency was constructed to be exactly 40 ms. The new method accurately indicated the value of the simulated reflex latency (40 ms. However, the classical method showed that the lag time between the simulated triggers and the simulated signals was 49 ms. Simulation results illustrated that the cumulated average method is a reliable and more accurate method compared with the classical method. We therefore suggest that the new cumulated average method is able to determine the high rate stimulation induced reflex latencies more accurately than the classical method.

  15. Event Detection and Sub-state Discovery from Bio-molecular Simulations Using Higher-Order Statistics: Application To Enzyme Adenylate Kinase

    OpenAIRE

    Ramanathan, Arvind; Savol, Andrej J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

    2012-01-01

    Biomolecular simulations at milli-second and longer timescales can provide vital insights into functional mechanisms. Since post-simulation analyses of such large trajectory data-sets can be a limiting factor in obtaining biological insights, there is an emerging need to identify key dynamical events and relating these events to the biological function online, that is, as simulations are progressing. Recently, we have introduced a novel computational technique, quasi-anharmonic analysis (QAA)...

  16. Determination of the decomposition products of Usal in model systems and determination of dioxopiperazine in soft drinks by HPLC.

    Science.gov (United States)

    Prudel, M; Davídková, E

    1985-01-01

    A HPLC method for the determination of Usal (Aspartame hydrochloride, L-aspartyl-L-phenylalanine methyl ester hydrochloride) and its decomposition products was elaborated. Aspartic acid, phenylalanine, phenylalanine methyl ester, aspartyl-phenylalanine, phenylalanyl-aspartic acid, 5-benzyl-3,6-dioxo-2-piperazineacetic acid (DOP) and Usal were separated on Separon SI C-18. The mobile phase was: 0.5 M NaH2PO4 (pH 2.1) and methanol (85:15 v/v). The detection was carried out at 200 nm. The method for DOP determination was tested by the analysis of 10 types of soft drinks to which DOP was added. In two newly developed sorts of soft drinks sweetened with Usal the formation of DOP was followed during storage. The DOP increment after 34 days of storage reached 0.7 and 6 mg/l at 7 and 20 degrees C, resp. The method is also suitable for DOP determination in the sweetener itself. PMID:4022104

  17. Reproducibility - an important factor determining the quality of computer aided detection (CAD) systems

    International Nuclear Information System (INIS)

    Purpose: To test the reproducibility of markings on mammography films set by a commercial computer aided detection (CAD) system. Patients and methods: One hundred unilateral mammography examinations (each in CC and MLO) of 100 patients with mammographically detected suspicious foci, which were histopathologically proven to be malignant, were scanned three times with the CAD system, retrospectively. Every fifth patient of the institutional tumor case sampler was enrolled in the study. Only cases with one visible lesion were included in the study. Reproducibility and sensitivity (in both the strict and the broader sense) were determined. Strict sensitivity means the correct set of markers in both images, whereas broader sensitivity means the correct set in at least one of the images. Sixteen of 100 malignancies were indicated by focal suspicious microcalcification clusters, 53 tumors by masses and 31 cases by both signs of breast cancer. The CAD evaluation was divided into only two different markers: one for microcalcifications and one for masses. Thus, 47 (16+31) tumor-induced microcalcifications and 84 (53+31) malignancy-related masses were checked using the CAD system. Results: Eighteen of 100 unilateral mammography examinations revealed identical patterns in all three scans (18% reproducibility). Eleven of 47 suspicious focal microcalcification clusters and 43/84 masses were correctly marked on both mammographic views in all three CAD scans (strict and broader sensitivity, 23.4 and 51.1%, respectively). Six of 47 microcalcification clusters and 8/84 masses were totally missed in all images by the system (false negative rate, 12.8 and 9.6%, respectively). Conclusion: Reproducibility is essential for CAD systems. Currently, reproducibility of the used CAD system appears to be insufficient for clinical routine. Improvement of the system characteristics would make such systems valuable as a 'second reader' in clinical examination

  18. 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.

  19. A method to determine rapidty the cocrystallization coefficient of slightly soluble substances in open systems

    International Nuclear Information System (INIS)

    The technique of rapid determination of the equilibrium coefficient D of cocrystallization admixture with a macrocomponent (a slightly soluble compound) is developed. A certain portion containing micro- andnd macrocomponents is periodically taken from a mixed suspension and instead micro- and macrocomponents in the same amounts are added to the suspension. The macrocomponent is added as aqueous solutions of reagents which give an appropriate precipitate during interaction. The mathematical explanation of the method is given. The method is tested for the determination of D value in the 152Eu (3) (microcomponent)-ZnC2O4x2H2O (macrocomponent) H2O system. It is found that at pH-4, 25 deg C and ionic force, corresponding to 0.05 mol/l HCl solution the equilibrium value D=(3.4+-0.1)x10-3 is reached following 10 hours after the experiment beginning

  20. 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.

  1. Automatic ultrasonic inspection system for wear determination in calandria tubes of Embalse Nuclear Power Plant

    International Nuclear Information System (INIS)

    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

  2. Wind direction over the ocean determined by an airborne, imaging, polarimetric radiometer system

    DEFF Research Database (Denmark)

    Laursen, Brian; Skou, Niels

    2001-01-01

    The speed and direction of winds over the ocean can be determined by polarimetric radiometers. This has been established by theoretical work and demonstrated experimentally using airborne radiometers carrying out circle flights and thus measuring the full 360° azimuthal response from the sea...... surface. An airborne experiment, with the aim of measuring wind direction over the ocean using an imaging polarimetric radiometer, is described. A polarimetric radiometer system of the correlation type, measuring all four Stokes brightness parameters, is used. Imaging is achieved using a 1-m aperture...... conically scanning antenna. The polarimetric azimuthal signature of the ocean is known from modeling and circle flight experiments. Combining the signature with the measured brightness data from just a single flight track enables the wind direction to be determined on a pixel-by-pixel basis in the...

  3. 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.

  4. Potassium permanganate-glutaraldehyde chemiluminescence system catalyzed by gold nanoprisms toward selective determination of fluoride.

    Science.gov (United States)

    Abolhasani, Jafar; Hassanzadeh, Javad; Ghorbani-Kalhor, Ebrahim

    2016-02-01

    Gold and silver nanoparticles (NPs) are shown to exert a positive effect on the chemiluminescence (CL) reaction of permanganate aldehydes. Interestingly, between various shapes examined, Au nanoprisms have the highest beneficial effect. This effect is even more notable in the presence of sodium dodecyl sulfate (SDS) surfactant. UV-vis spectra and transmission electron microscopy were used to characterize the NP shapes and sizes. Furthermore, it was observed that iron(III) ions can slightly increase CL emission of this system. This intensification is very effective in the presence of fluoride ions (F(-)). These observations form the basis of the method for the high sensitive determination of F(-) in the 6-1200 nmol L(-1) concentration range, with a detection limit of 2.1 nmol L(-1). The proposed method has good precision and was satisfactorily used in the selective determination of low concentrations of fluoride ion in real samples. PMID:26110514

  5. Automatic ultrasonic inspection system for wear determination in calandria tubes of Embalse Nuclear Power Plant

    Energy Technology Data Exchange (ETDEWEB)

    Katchadjian, Pablo, E-mail: katcha@cnea.gov.ar; Desimone, Carlos, E-mail: katcha@cnea.gov.ar; Garcia, Alejandro, E-mail: katcha@cnea.gov.ar [Comisión Nacional de Energía Atómica, Depto. ENDE - INEND, Av. Gral. Paz 1499, Buenos Aires (Argentina); Antonaccio, Carlos; Schroeter, Fernando; Molina, Héctor [Nucleoeléctrica Argentina-SA, Arribeños 3619, Buenos Aires (Argentina)

    2015-03-31

    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. Carrier-phase GNSS Attitude Determination and Control System for Unmanned Aerial Vehicle Applications

    Directory of Open Access Journals (Sweden)

    Roberto Sabatini, Leopoldo Rodríguez, Anish Kaharkar, Celia Bartel, Tesheen Shaid

    2012-12-01

    Full Text Available This paper presents the results of a research activity performed by Cranfield University to assess the potential of carrierphase Global Navigation Satellite Systems (GNSS for attitude determination and control of small to medium size Unmanned Aerial Vehicles (UAV. Both deterministic and recursive (optimal estimation algorithms are developed for combining multiple attitude measurements obtained from different observation points (i.e., antenna locations, and their efficiencies are tested in various dynamic conditions. The proposed algorithms converge rapidly and produce the required output even during high dynamics manoeuvres. Results of theoretical performance analysis and simulation activities are presented in this paper, with emphasis on the advantages of the GNSS interferometric approach in UAV applications (i.e., low cost, high data-rate, low volume/weight, low signal processing requirements, etc.. Modelling and simulation activities focussed on the AEROSONDE UAV platform and considered the possible augmentation provided by interferometric GNSS techniques to a low-cost and low-weight/volume integrated navigation system recently developed at Cranfield University, which employs a Vision-based Navigation (VBN system, a Micro-Electro-mechanical Sensor (MEMS based Inertial Measurement Unit (IMU and code-range GNSS (i.e., GPS and GALILEO for position and velocity computations. The integrated VBN-IMU-GNSS (VIG system is augmented by using the inteferometric GNSS Attitude Determination(GAD and a comparison of the performance achievable with the VIG and VIG/GAD integrated Navigation and Guidance Systems (NGS is presented. Finally, the data provided by these NGS are used to optimise the design of an hybrid controller employing Fuzzy Logic and Proportional-Integral-Derivative (PID techniques for the AEROSONDE UAV.

  7. Evaluation of the Geomagnetic Field Models based on Magnetometer Measurements for Satellite's Attitude Determination System

    Science.gov (United States)

    Cilden, Demet; Kaymaz, Zerefsan; Hajiyev, Chingiz

    2016-07-01

    Magnetometers are common attitude determination sensors for small satellites at low Earth orbit; therefore, magnetic field model of the Earth is necessary to estimate the satellite's attitude angles. Difference in the components of the magnetic field vectors -mostly used as unit vector. Therefore the angle between them (model and measurement data) affects the estimation accuracy of the satellite's attitude. In this study, geomagnetic field models are compared with satellite magnetic field observations in order to evaluate the models using the magnetometer results with high accuracy. For attitude determination system, IGRF model is used in most of the cases but the difference between the sensor and model increases when the geomagnetic activity occurs. Hence, several models including the empirical ones using the external variations in the Earth's geomagnetic field resulting from the solar wind and interplanetary magnetic field are of great importance in determination of the satellite's attitude correctly. IGRF model describes the internal-part of the geomagnetic field, on the other hand candidate models to IGRF, such as recently developed POMME-6 model based on Champ data, CHAOS-5 (CHAmp, Oersted, Swarm), T89 (Tsyganenko's model), include simple parameterizations of external fields of magnetospheric sources in addition to the internal field especially for low Earth orbiting satellites. Those models can be evaluated to see noticeable difference on extraterrestrial field effects on satellite's attitude determination system changing with its height. The comparisons are made between the models and observations and between the models under various magnetospheric activities. In this study, we will present our preliminary results from the comparisons and discuss their implications from the satellite attitude perspective.

  8. A MMC/MIMU/GPS integrated attitude and azimuth determination system

    Science.gov (United States)

    Sheng, Wei; Ma, Yanwu; Cao, Juanjuan

    2008-10-01

    Exact knowledge of attitude and azimuth is a fundamental factor in steering vehicle and robot (called carrier in this paper). Micro inertial measurement unit (MIMU), i.e. IMU made by silicon MEMS inertial sensors, GPS and MEMS magnetic compass (MMC), are often used in traditional low-cost attitude and azimuth determination solutions. The main discrepancy, in all of these low-cost approaches, is that the azimuth output is affected by acceleration and turns for long-playing carriers. This paper puts forward a MMC/MIMU/GPS integrated system and an iterative attitude & azimuth determination algorithm for long-playing accelerated carrier's motion. GPS output (.i.e. position and velocity), in ENU (East-North-Upward) navigation frame is transformed into body frame by transformation matrix Cbn. By integrating the MIMU and GPS measurements, through Kalman Filter (KF), the three orthogonal components of the gravity vector are precisely estimated in body frame despite the acceleration effects. Pitch and roll angles are calculated by gravity vector components in body frame, where as azimuth angle is calculated by combining pitch angle, roll angle and MMC output. The direction cosine matrix Cbn, updated by the latest azimuth, roll and pitch angles, is used in next round of this iterative attitude & azimuth determination algorithm. CFAR (Constant False Alarm Rate) filters have been utilized to suppress the noise in GPS data caused by differential operation. The proposed iterative algorithm has been practically implemented and simulated. The simulations results prove the ability of the MMC/MIMU/GPS integrated system to determine the attitude and azimuth for long-playing carrier in any motion situation.

  9. Determination of the critical micelle concentration in simulations of surfactant systems

    International Nuclear Information System (INIS)

    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. 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)

  11. Amperometric biosensor system for simultaneous determination of adenosine-5'-triphosphate and glucose.

    Science.gov (United States)

    Kucherenko, Ivan S; Didukh, Daria Yu; Soldatkin, Oleksandr O; Soldatkin, Alexei P

    2014-06-01

    The majority of biosensors for adenosine-5'-triphosphate (ATP) determination are based on cascades of enzymatic reactions; therefore, they are sensitive to glucose or glycerol (depending on the enzymatic system) as well as to ATP. The presence of unknown concentrations of these substances in the sample greatly complicates the determination of ATP. To overcome this disadvantage of known biosensors, we developed a biosensor system consisting of two biosensors: the first one is based on glucose oxidase and is intended for measuring glucose concentration, and the second one is based on glucose oxidase and hexokinase and is sensitive toward both glucose and ATP. Using glucose concentration measured by the first biosensor, we can analyze the total response to glucose and ATP obtained by the second biosensor. Platinum disc electrodes were used as amperometric transducers. The polyphenilenediamine membrane was deposited onto the surface of platinum electrodes to avoid the response to electroactive substances. The effect of glucose concentration on biosensor determination of ATP was studied. The reproducibility of biosensor responses to glucose and ATP during a day was tested (relative standard deviation, RSD, of responses to glucose was 3-6% and to ATP was 8-12%) as well as storage stability of the biosensors (no decrease of glucose responses and 43% drop of ATP responses during 50 days). The measurements of ATP and glucose in pharmaceutical vials (including mixtures of ATP and glucose) were carried out. It was shown that the developed biosensor system can be used for simultaneous analysis of glucose and ATP concentrations in water solutions. PMID:24810180

  12. Non-Ewald methods: theory and applications to molecular systems

    OpenAIRE

    Fukuda, Ikuo; Nakamura, Haruki

    2012-01-01

    Several non-Ewald methods for calculating electrostatic interactions have recently been developed, such as the Wolf method, the reaction field method, the pre-averaging method, and the zero-dipole summation method, for molecular dynamics simulations of various physical systems, including biomolecular systems. We review the theories of these approaches and their potential applications to molecular simulations, and discuss their relationships.

  13. Reactivity and kinetic parameters determination in a multiplicative non-stationary system

    International Nuclear Information System (INIS)

    A revision of several methods used for solving kinetic equations of a neutronic system is considered. Firstly, kinetic equations in general form are analized, before to revise more important aproximations: point-kinetic method; adiabatic; cuasistatic; eigenvalue equations; nodal, modal and systhesis methods; and variational principles for obtaining kinetic equations. Perturbation theory is used to obtain these parameters, with differents eigenvalue equations representatives of the parameter to be calculated. Also, experimental methods have been included in this work, because of importance the parameters can be measured, and related with those obtained by calculations. Finally, adjoint kinetic equations are resolved to obtain the importance function used in weighted reactivity and kinetic parameters determinations. (author)

  14. Determination of microelement distribution in different components of soil-plant system

    International Nuclear Information System (INIS)

    Leaves, stem, and roots of two shrub types: tea (Camellia sinensis), sweet leaf (Sauropus androgynus) and two herb types: vetiver grass (Vetiveria zizanioides L.Nash), maize (Zea mays L) and Thucuc soil where the plants grow, were collected to be studied. Contents of 22 elements in the samples were determined by three methods: XRFA (X-Ray Fluorescence Analysis), GAA (Gamma Activation Analysis), and tracking method to study distribution of these elements in plants and soil-plant relationship. The study was carried out at the Flerov Laboratory of Nuclear Reactions, JINR, Dubna. Distribution of the elements in the soil-plant system was studied

  15. Improved treatment of global positioning system force parameters in precise orbit determination applications

    Science.gov (United States)

    Vigue, Y.; Lichten, S. M.; Muellerschoen, R. J.; Blewitt, G.; Heflin, M. B.

    1993-01-01

    Data collected from a worldwide 1992 experiment were processed at JPL to determine precise orbits for the satellites of the Global Positioning System (GPS). A filtering technique was tested to improve modeling of solar-radiation pressure force parameters for GPS satellites. The new approach improves orbit quality for eclipsing satellites by a factor of two, with typical results in the 25- to 50-cm range. The resultant GPS-based estimates for geocentric coordinates of the tracking sites, which include the three DSN sites, are accurate to 2 to 8 cm, roughly equivalent to 3 to 10 nrad of angular measure.

  16. Use of Equipment Information System (EQUIS) to determine priority for purchasing safeguards equipment

    International Nuclear Information System (INIS)

    To manage its large world-wide inventory of safeguards equipment, the IAEA Safeguards department uses a computerized Equipment Information System (EQUIS). EQUIS data have been analyzed using Queueing Theory to determine if inventory is adequate to meet inspector demands and in those cases where it is inadequate, to indicate how many additional units should be procured. Results are tabulated for various types of non-destructive analysis (NDA) equipment. For equipment where there is a high turnover and hence a large amount of data, the analysis provides a powerful tool for assisting procurement decisions

  17. Determination of generator groupings for an islanding scheme in the Manitoba Hydro system using the method of normal forms

    OpenAIRE

    Vittal, V; Kliemann, W; Chapman, DG; Silk, AD; Sobajic, DJ; Ni, Y.

    1998-01-01

    This paper deals with the application of the method of normal forms in the analysis of a specific aspect of system dynamic behavior in the Manitoba Hydro system. Following a major loss of transmission capacity on the Manitoba Hydro HVDC system (Nelson River system), and the subsequent operation of protection systems, there is a major deficit of generation in the remaining system, comprising Manitoba and Saskatchewan. The method of normal forms is applied to determine the natural groupings whi...

  18. The Icebreaker Life Mission to Mars: a search for biomolecular evidence for life.

    Science.gov (United States)

    McKay, Christopher P; Stoker, Carol R; Glass, Brian J; Davé, Arwen I; Davila, Alfonso F; Heldmann, Jennifer L; Marinova, Margarita M; Fairen, Alberto G; Quinn, Richard C; Zacny, Kris A; Paulsen, Gale; Smith, Peter H; Parro, Victor; Andersen, Dale T; Hecht, Michael H; Lacelle, Denis; Pollard, Wayne H

    2013-04-01

    The search for evidence of life on Mars is the primary motivation for the exploration of that planet. The results from previous missions, and the Phoenix mission in particular, indicate that the ice-cemented ground in the north polar plains is likely to be the most recently habitable place that is currently known on Mars. The near-surface ice likely provided adequate water activity during periods of high obliquity, ≈ 5 Myr ago. Carbon dioxide and nitrogen are present in the atmosphere, and nitrates may be present in the soil. Perchlorate in the soil together with iron in basaltic rock provides a possible energy source for life. Furthermore, the presence of organics must once again be considered, as the results of the Viking GCMS are now suspect given the discovery of the thermally reactive perchlorate. Ground ice may provide a way to preserve organic molecules for extended periods of time, especially organic biomarkers. The Mars Icebreaker Life mission focuses on the following science goals: (1) Search for specific biomolecules that would be conclusive evidence of life. (2) Perform a general search for organic molecules in the ground ice. (3) Determine the processes of ground ice formation and the role of liquid water. (4) Understand the mechanical properties of the martian polar ice-cemented soil. (5) Assess the recent habitability of the environment with respect to required elements to support life, energy sources, and possible toxic elements. (6) Compare the elemental composition of the northern plains with midlatitude sites. The Icebreaker Life payload has been designed around the Phoenix spacecraft and is targeted to a site near the Phoenix landing site. However, the Icebreaker payload could be supported on other Mars landing systems. Preliminary studies of the SpaceX Dragon lander show that it could support the Icebreaker payload for a landing either at the Phoenix site or at midlatitudes. Duplicate samples could be cached as a target for possible return by

  19. DETERMINING THE THERMAL RESISTANCE OF A VENTILATED HINGED FACADE SYSTEM LAYER

    Directory of Open Access Journals (Sweden)

    Gagarin Vladimir Gennad'evich

    2015-03-01

    Full Text Available Enveloping structures with hinged façade systems are nowadays widely used for moisture control of enveloping structures, prevention of overheating of the structures by insolation, saving the constructions from atmospheric moisture and also for correspondence with the raised requirements to thermal protection of the enveloping structures, aimed also at reducing energy consumption. In the winter conditions the influence of air layer on the thermal insulation parameters is usually neglected. In the article the thermal resistance of an air gap and is considered and its effect in the calculation of the heat resistance of a building envelope with hinged facade system is analyzed in the conditions of cold weather. The thermal resistance of the air layer determines how the heat losses decrease.

  20. 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.