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. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biomolecular simulations on petascale: promises and challenges

International Nuclear Information System (INIS)

Agarwal, Pratul K; Alam, Sadaf R

2006-01-01

Proteins work as highly efficient machines at the molecular level and are responsible for a variety of processes in all living cells. There is wide interest in understanding these machines for implications in biochemical/biotechnology industries as well as in health related fields. Over the last century, investigations of proteins based on a variety of experimental techniques have provided a wealth of information. More recently, theoretical and computational modeling using large scale simulations is providing novel insights into the functioning of these machines. The next generation supercomputers with petascale computing power, hold great promises as well as challenges for the biomolecular simulation scientists. We briefly discuss the progress being made in this area

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.

Biomolecular engineering for nanobio/bionanotechnology

Science.gov (United States)

Nagamune, Teruyuki

2017-04-01

Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.

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

National Research Council Canada - National Science Library

Frazier, John; Chusak, Yaroslav; Foy, Brent

2008-01-01

.... The software uses either exact or approximate stochastic simulation algorithms for generating Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks...

Biomolecular structure refinement using the GROMOS simulation software

International Nuclear Information System (INIS)

Schmid, Nathan; Allison, Jane R.; Dolenc, Jožica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van

2011-01-01

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, 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.

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.

A statistical nanomechanism of biomolecular patterning actuated by surface potential

Science.gov (United States)

Lin, Chih-Ting; Lin, Chih-Hao

2011-02-01

Biomolecular patterning on a nanoscale/microscale on chip surfaces is one of the most important techniques used in vitro biochip technologies. Here, we report upon a stochastic mechanics model we have developed for biomolecular patterning controlled by surface potential. The probabilistic biomolecular surface adsorption behavior can be modeled by considering the potential difference between the binding and nonbinding states. To verify our model, we experimentally implemented a method of electroactivated biomolecular patterning technology and the resulting fluorescence intensity matched the prediction of the developed model quite well. Based on this result, we also experimentally demonstrated the creation of a bovine serum albumin pattern with a width of 200 nm in 5 min operations. This submicron noncovalent-binding biomolecular pattern can be maintained for hours after removing the applied electrical voltage. These stochastic understandings and experimental results not only prove the feasibility of submicron biomolecular patterns on chips but also pave the way for nanoscale interfacial-bioelectrical engineering.

NMRbox: A Resource for Biomolecular NMR Computation.

Science.gov (United States)

Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

2017-04-25

Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

Selected topics in solution-phase biomolecular NMR spectroscopy

Science.gov (United States)

Kay, Lewis E.; Frydman, Lucio

2017-05-01

Solution bio-NMR spectroscopy continues to enjoy a preeminent role as an important tool in elucidating the structure and dynamics of a range of important biomolecules and in relating these to function. Equally impressive is how NMR continues to 'reinvent' itself through the efforts of many brilliant practitioners who ask increasingly demanding and increasingly biologically relevant questions. The ability to manipulate spin Hamiltonians - almost at will - to dissect the information of interest contributes to the success of the endeavor and ensures that the NMR technology will be well poised to contribute to as yet unknown frontiers in the future. As a tribute to the versatility of solution NMR in biomolecular studies and to the continued rapid advances in the field we present a Virtual Special Issue (VSI) that includes over 40 articles on various aspects of solution-state biomolecular NMR that have been published in the Journal of Magnetic Resonance in the past 7 years. These, in total, help celebrate the achievements of this vibrant field.

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...

A model system for targeted drug release triggered by biomolecular signals logically processed through enzyme logic networks.

Science.gov (United States)

Mailloux, Shay; Halámek, Jan; Katz, Evgeny

2014-03-07

A new Sense-and-Act system was realized by the integration of a biocomputing system, performing analytical processes, with a signal-responsive electrode. A drug-mimicking release process was triggered by biomolecular signals processed by different logic networks, including three concatenated AND logic gates or a 3-input OR logic gate. Biocatalytically produced NADH, controlled by various combinations of input signals, was used to activate the electrochemical system. A biocatalytic electrode associated with signal-processing "biocomputing" systems was electrically connected to another electrode coated with a polymer film, which was dissolved upon the formation of negative potential releasing entrapped drug-mimicking species, an enzyme-antibody conjugate, operating as a model for targeted immune-delivery and consequent "prodrug" activation. The system offers great versatility for future applications in controlled drug release and personalized medicine.

Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

Science.gov (United States)

Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

2013-01-01

Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

Science.gov (United States)

Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron; Gümüs, Zeynep H

2017-08-01

Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. © The Authors 2017. Published by Oxford University Press.

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

Programming in biomolecular computation

DEFF Research Database (Denmark)

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

2011-01-01

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

Improvements to the APBS biomolecular solvation software suite.

Science.gov (United States)

Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

2018-01-01

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks.

Science.gov (United States)

Papini, Christina; Royer, Catherine A

2018-02-01

Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.

Biomolecular electrostatics and solvation: a computational perspective.

Science.gov (United States)

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

2012-11-01

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

Membrane-based biomolecular smart materials

International Nuclear Information System (INIS)

Sarles, Stephen A; Leo, Donald J

2011-01-01

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

Investigating biomolecular recognition at the cell surface using atomic force microscopy.

Science.gov (United States)

Wang, Congzhou; Yadavalli, Vamsi K

2014-05-01

Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique. Copyright © 2014 Elsevier Ltd. All rights reserved.

Conducting polymer based biomolecular electronic devices

Indian Academy of Sciences (India)

Conducting polymers; LB films; biosensor microactuators; monolayers. ... have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices.

Aligning Biomolecular Networks Using Modular Graph Kernels

Science.gov (United States)

Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

Biomolecular simulation: historical picture and future perspectives.

Science.gov (United States)

van Gunsteren, Wilfred F; Dolenc, Jozica

2008-02-01

Over the last 30 years, computation based on molecular models is playing an increasingly important role in biology, biological chemistry and biophysics. Since only a very limited number of properties of biomolecular systems are actually accessible to measurement by experimental means, computer simulation complements experiments by providing not only averages, but also distributions and time series of any definable, observable or non-observable, quantity. Biomolecular simulation may be used (i) to interpret experimental data, (ii) to provoke new experiments, (iii) to replace experiments and (iv) to protect intellectual property. Progress over the last 30 years is sketched and perspectives are outlined for the future.

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.

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. Copyright © 2013 Elsevier B.V. All rights reserved.

Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

Science.gov (United States)

Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

2017-08-30

A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

Application of Hidden Markov Models in Biomolecular Simulations.

Science.gov (United States)

Shukla, Saurabh; Shamsi, Zahra; Moffett, Alexander S; Selvam, Balaji; Shukla, Diwakar

2017-01-01

Hidden Markov models (HMMs) provide a framework to analyze large trajectories of biomolecular simulation datasets. HMMs decompose the conformational space of a biological molecule into finite number of states that interconvert among each other with certain rates. HMMs simplify long timescale trajectories for human comprehension, and allow comparison of simulations with experimental data. In this chapter, we provide an overview of building HMMs for analyzing bimolecular simulation datasets. We demonstrate the procedure for building a Hidden Markov model for Met-enkephalin peptide simulation dataset and compare the timescales of the process.

Dynamic and label-free high-throughput detection of biomolecular interactions based on phase-shift interferometry

Science.gov (United States)

Li, Qiang; Huang, Guoliang; Gan, Wupeng; Chen, Shengyi

2009-08-01

Biomolecular interactions can be detected by many established technologies such as fluorescence imaging, surface plasmon resonance (SPR)[1-4], interferometry and radioactive labeling of the analyte. In this study, we have designed and constructed a label-free, real-time sensing platform and its operating imaging instrument that detects interactions using optical phase differences from the accumulation of biological material on solid substrates. This system allows us to monitor biomolecular interactions in real time and quantify concentration changes during micro-mixing processes by measuring the changes of the optical path length (OPD). This simple interferometric technology monitors the optical phase difference resulting from accumulated biomolecular mass. A label-free protein chip that forms a 4×4 probe array was designed and fabricated using a commercial microarray robot spotter on solid substrates. Two positive control probe lines of BSA (Bovine Serum Albumin) and two experimental human IgG and goat IgG was used. The binding of multiple protein targets was performed and continuously detected by using this label-free and real-time sensing platform.

Application of Nanodiamonds in Biomolecular Mass Spectrometry

Directory of Open Access Journals (Sweden)

Ping Cheng

2010-03-01

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

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

is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology......Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... 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...

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...

Unique temporal and spatial biomolecular emission profile on individual zinc oxide nanorods

Science.gov (United States)

Singh, Manpreet; Song, Sheng; Hahm, Jong-In

2013-12-01

signal-enhancing platforms in DNA and protein detection. Although the use of ZnO NRs in biodetection has been demonstrated so far in systems involving many ZnO NRs per detection element, their future applications will likely take place in a miniaturized setting while exploiting single ZnO NRs in a low-volume, high-throughput bioanalysis. In this paper, we investigate temporal and spatial characteristics of the biomolecular fluorescence on individual ZnO NR systems. Quantitative and qualitative examinations of the biomolecular intensity and photostability are carried out as a function of two important criteria, the time and position along the long axis (length) of NRs. Photostability profiles are also measured with respect to the position on NRs and compared to those characteristics of biomolecules on polymeric control platforms. Unlike the uniformly distributed signal observed on the control platforms, both the fluorescence intensity and photostability are position-dependent on individual ZnO NRs. We have identified a unique phenomenon of highly localized, fluorescence intensification on the nanorod ends (FINE) of well-characterized, individual ZnO nanostructures. When compared to the polymeric controls, the biomolecular fluorescence intensity and photostability are determined to be higher on individual ZnO NRs regardless of the position on NRs. We have also carried out finite-difference time-domain simulations the results of which are in good agreement with the observed FINE. The outcomes of our investigation will offer a much needed basis for signal interpretation for biodetection devices and platforms consisting of single ZnO NRs and, at the same time, contribute significantly to provide insight in understanding the biomolecular fluorescence observed from ZnO NR ensemble-based systems. Electronic supplementary information (ESI) available: ZnO NR size distributions, a FINE image from fluorophores on ZnO NR without protein coupling, and FDTD simulation movies. See DOI

XML-based approaches for the integration of heterogeneous bio-molecular data.

Science.gov (United States)

Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

2009-10-15

The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

Science.gov (United States)

Xu, Yao; Havenith, Martina

2015-11-01

Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

Modeling, Analysis, Simulation, and Synthesis of Biomolecular Networks

National Research Council Canada - National Science Library

Ruben, Harvey; Kumar, Vijay; Sokolsky, Oleg

2006-01-01

...) a first example of reachability analysis applied to a biomolecular system (lactose induction), 4) a model of tetracycline resistance that discriminates between two possible mechanisms for tetracycline diffusion through the cell membrane, and 5...

A compact hard X-ray source for medical imaging and biomolecular studies

International Nuclear Information System (INIS)

Cline, D.B.; Green, M.A.; Kolonko, J.

1995-01-01

There are a large number of synchrotron light sources in the world. However, these sources are designed for physics, chemistry, and engineering studies. To our knowledge, none have been optimized for either medical imaging or biomolecular studies. There are special needs for these applications. We present here a preliminary design of a very compact source, small enough for a hospital or a biomolecular laboratory, that is suitable for these applications. (orig.)

Ion induced fragmentation of biomolecular systems at low collision energies

International Nuclear Information System (INIS)

Bernigaud, V; Adoui, L; Chesnel, J Y; Rangama, J; Huber, B A; Manil, B; Alvarado, F; Bari, S; Hoekstra, R; Postma, J; Schlathoelter, T

2009-01-01

In this paper, we present results of different collision experiments between multiply charged ions at low collision energies (in the keV-region) and biomolecular systems. This kind of interaction allows to remove electrons form the biomolecule without transferring a large amount of vibrational excitation energy. Nevertheless, following the ionization of the target, fragmentation of biomolecular species may occur. It is the main objective of this work to study the physical processes involved in the dissociation of highly electronically excited systems. In order to elucidate the intrinsic properties of certain biomolecules (porphyrins and amino acids) we have performed experiments in the gas phase with isolated systems. The obtained results demonstrate the high stability of porphyrins after electron removal. Furthermore, a dependence of the fragmentation pattern produced by multiply charged ions on the isomeric structure of the alanine molecule has been shown. By considering the presence of other surrounding biomolecules (clusters of nucleobases), a strong influence of the environment of the biomolecule on the fragmentation channels and their modification, has been clearly proven. This result is explained, in the thymine and uracil case, by the formation of hydrogen bonds between O and H atoms, which is known to favor planar cluster geometries.

PREFACE: Radiation Damage in Biomolecular Systems (RADAM07)

Science.gov (United States)

McGuigan, Kevin G.

2008-03-01

, which include: theoretical, experimental, medical and computational physicists, radiation chemists, radiation biologists and microbiologists, among others. An important aspect of the previous 3 conferences in this series was to remove barriers between the different working groups and to encourage a more interdisciplinary approach to research collaborations. During RADAM_07 we could observe the success of these efforts. A large number of presentations were based on new collaborations, many funded under the COST STSM programme, and all presentations led to lively discussions. It is clear from the discussions following many of the presentations and at the poster sessions that Radiation Damage in Biomolecular Systems remains a topic of increasing interest, relevance and importance. The success of this conference as well as of the whole RADAM conference series reflects the growing international interest in the area of interactions of ionizing radiation with biomolecules. Despite the scheduled conclusion in September 2007 of COST Action P9 which has part-funded this, and previous RADAM meetings, the nature of the cross-disciplinary interactions and opportunities for collaborative research was deemed so successful and valuable by the assembled delegates that it was agreed that another such meeting should be held in Debrecen in Hungary from 13-15 June 2008 http://www.isa.au.dk/meetings/radam2008/programme.html. Additional information about RADAM07 programme is available on the conference web-page http://www.isa.au.dk/networks/cost/radam07/index.html. The Organizing Committee would like to thank all speakers, contributors, session chairs, referees and meeting staff for their efforts in making the RADAM07 successful. The local Organization Committee would like to thank Lorraine Monard and Margaret Nolan for their invaluable expertise in conference management. We also gratefully acknowledge the financial support of our sponsors - The Royal, College of Surgeons in Ireland (RCSI

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.

Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

Energy Technology Data Exchange (ETDEWEB)

Jurrus, Elizabeth [Pacific Northwest National Laboratory, Richland Washington; Engel, Dave [Pacific Northwest National Laboratory, Richland Washington; Star, Keith [Pacific Northwest National Laboratory, Richland Washington; Monson, Kyle [Pacific Northwest National Laboratory, Richland Washington; Brandi, Juan [Pacific Northwest National Laboratory, Richland Washington; Felberg, Lisa E. [University of California, Berkeley California; Brookes, David H. [University of California, Berkeley California; Wilson, Leighton [University of Michigan, Ann Arbor Michigan; Chen, Jiahui [Southern Methodist University, Dallas Texas; Liles, Karina [Pacific Northwest National Laboratory, Richland Washington; Chun, Minju [Pacific Northwest National Laboratory, Richland Washington; Li, Peter [Pacific Northwest National Laboratory, Richland Washington; Gohara, David W. [St. Louis University, St. Louis Missouri; Dolinsky, Todd [FoodLogiQ, Durham North Carolina; Konecny, Robert [University of California San Diego, San Diego California; Koes, David R. [University of Pittsburgh, Pittsburgh Pennsylvania; Nielsen, Jens Erik [Protein Engineering, Novozymes A/S, Copenhagen Denmark; Head-Gordon, Teresa [University of California, Berkeley California; Geng, Weihua [Southern Methodist University, Dallas Texas; Krasny, Robert [University of Michigan, Ann Arbor Michigan; Wei, Guo-Wei [Michigan State University, East Lansing Michigan; Holst, Michael J. [University of California San Diego, San Diego California; McCammon, J. Andrew [University of California San Diego, San Diego California; Baker, Nathan A. [Pacific Northwest National Laboratory, Richland Washington; Brown University, Providence Rhode Island

2017-10-24

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

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

International Nuclear Information System (INIS)

Kyu Kim, Sang; Cho, Hyunmin; Park, Hye-Jung; Kwon, Dohyoung; Min Lee, Jeong; Hyun Chung, Bong

2009-01-01

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

Review of MEMS differential scanning calorimetry for biomolecular study

Science.gov (United States)

Yu, Shifeng; Wang, Shuyu; Lu, Ming; Zuo, Lei

2017-12-01

Differential scanning calorimetry (DSC) is one of the few techniques that allow direct determination of enthalpy values for binding reactions and conformational transitions in biomolecules. It provides the thermodynamics information of the biomolecules which consists of Gibbs free energy, enthalpy and entropy in a straightforward manner that enables deep understanding of the structure function relationship in biomolecules such as the folding/unfolding of protein and DNA, and ligand bindings. This review provides an up to date overview of the applications of DSC in biomolecular study such as the bovine serum albumin denaturation study, the relationship between the melting point of lysozyme and the scanning rate. We also introduce the recent advances of the development of micro-electro-mechanic-system (MEMS) based DSCs.

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, 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.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

Directory of Open Access Journals (Sweden)

Clarisse Gravina Ricci

2018-02-01

Full Text Available Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.

Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

Science.gov (United States)

Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

2018-01-01

Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

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

International Nuclear Information System (INIS)

Zhou, Peipei; Cai, Shuiming; Liu, Zengrong; Chen, Luonan; Wang, Ruiqi

2013-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Zhou, Peipei [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Cai, Shuiming [Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Liu, Zengrong [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Chen, Luonan [Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Center for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan); Wang, Ruiqi [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China)

2013-05-15

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.

DNA algorithms of implementing biomolecular databases on a biological computer.

Science.gov (United States)

Chang, Weng-Long; Vasilakos, Athanasios V

2015-01-01

In this paper, DNA algorithms are proposed to perform eight operations of relational algebra (calculus), which include Cartesian product, union, set difference, selection, projection, intersection, join, and division, on biomolecular relational databases.

Smartphones for cell and biomolecular detection.

Science.gov (United States)

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

2014-11-01

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

Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches

Directory of Open Access Journals (Sweden)

Max Hirte

2018-04-01

restricted location of the enzyme's active site and that the geranylgeranyl diphosphate derived pyrophosphate moiety remains in the ACS active site thereby directing the cyclization process. Our cumulative data confirm that amino acids constituting the G-loop of diterpene synthases are involved in the open to the closed, catalytically active enzyme conformation. This study demonstrates that a simple and rapid biomolecular modeling procedure can predict catalytically relevant amino acids. The approach reduces computational and experimental screening efforts for diterpene synthase structure-function analyses.

Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches.

Science.gov (United States)

Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B

2018-01-01

the enzyme's active site and that the geranylgeranyl diphosphate derived pyrophosphate moiety remains in the ACS active site thereby directing the cyclization process. Our cumulative data confirm that amino acids constituting the G-loop of diterpene synthases are involved in the open to the closed, catalytically active enzyme conformation. This study demonstrates that a simple and rapid biomolecular modeling procedure can predict catalytically relevant amino acids. The approach reduces computational and experimental screening efforts for diterpene synthase structure-function analyses.

Insights into the bifunctional Aphidicolan-16-ß-ol synthase through rapid biomolecular modelling approaches

Science.gov (United States)

Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B.

2018-04-01

of the enzyme’s active site and that the geranylgeranyl diphosphate derived pyrophosphate moiety remains in the ACS active site thereby directing the cyclization process. Our cumulative data confirm that amino acids constituting the G-loop of diterpene synthases are involved in the open to the closed, catalytically active enzyme conformation. This study demonstrates that a simple and rapid biomolecular modelling procedure can predict catalytically relevant amino acids. The approach reduces computational and experimental screening efforts for diterpene synthase structure-function analyses.

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

Directory of Open Access Journals (Sweden)

Xiliang Zheng

2015-04-01

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

The HADDOCK web server for data-driven biomolecular docking

NARCIS (Netherlands)

de Vries, S.J.|info:eu-repo/dai/nl/304837717; van Dijk, M.|info:eu-repo/dai/nl/325811113; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

2010-01-01

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

GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

NARCIS (Netherlands)

Eichenberger, A.P.; Allison, J.R.; Dolenc, J.; Geerke, D.P.; Horta, B.A.C.; Meier, K; Oostenbrink, B.C.; Schmid, N.; Steiner, D; Wang, D.; van Gunsteren, W.F.

2011-01-01

GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular Simulation software for (bio)molecular simulation. It contains more than 70 programs that can be used to prepare data for the production of

Design rules for biomolecular adhesion: lessons from force measurements.

Science.gov (United States)

Leckband, Deborah

2010-01-01

Cell adhesion to matrix, other cells, or pathogens plays a pivotal role in many processes in biomolecular engineering. Early macroscopic methods of quantifying adhesion led to the development of quantitative models of cell adhesion and migration. The more recent use of sensitive probes to quantify the forces that alter or manipulate adhesion proteins has revealed much greater functional diversity than was apparent from population average measurements of cell adhesion. This review highlights theoretical and experimental methods that identified force-dependent molecular properties that are central to the biological activity of adhesion proteins. Experimental and theoretical methods emphasized in this review include the surface force apparatus, atomic force microscopy, and vesicle-based probes. Specific examples given illustrate how these tools have revealed unique properties of adhesion proteins and their structural origins.

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

Biomolecular bases of the senescence process and cancer. A new approach to oncological treatment linked to ageing.

Science.gov (United States)

Badiola, Iker; Santaolalla, Francisco; Garcia-Gallastegui, Patricia; Ana, Sánchez-Del Rey; Unda, Fernando; Ibarretxe, Gaskon

2015-09-01

Human ageing is associated with a gradual decline in the physiological functions of the body at multiple levels and it is a key risk factor for many diseases, including cancer. Ageing process is intimately related to widespread cellular senescence, characterised by an irreversible loss of proliferative capacity and altered functioning associated with telomere attrition, accumulation of DNA damage and compromised mitochondrial and metabolic function. Tumour and senescent cells may be generated in response to the same stimuli, where either cellular senescence or transformation would constitute two opposite outcomes of the same degenerative process. This paper aims to review the state of knowledge on the biomolecular relationship between cellular senescence, ageing and cancer. Importantly, many of the cell signalling pathways that are found to be altered during both cellular senescence and tumourigenesis are regulated through shared epigenetic mechanisms and, therefore, they are potentially reversible. MicroRNAs are emerging as pivotal players linking ageing and cancer. These small RNA molecules have generated great interest from the point of view of future clinical therapy for cancer because successful experimental results have been obtained in animal models. Micro-RNA therapies for cancer are already being tested in clinical phase trials. These findings have potential importance in cancer treatment in aged people although further research-based knowledge is needed to convert them into an effective molecular therapies for cancer linked to ageing. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

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.

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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...

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

Science.gov (United States)

Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

2014-06-14

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

An effective hierarchical model for the biomolecular covalent bond: an approach integrating artificial chemistry and an actual terrestrial life system.

Science.gov (United States)

Oohashi, Tsutomu; Ueno, Osamu; Maekawa, Tadao; Kawai, Norie; Nishina, Emi; Honda, Manabu

2009-01-01

Under the AChem paradigm and the programmed self-decomposition (PSD) model, we propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the PSD mechanism of turning biological polymers (BPs) into biological monomers (BMs) as an efficient biomolecular recycling strategy We have examined the validity and effectiveness of the HBCB model by coordinating two complementary approaches: biological experiments using existent terrestrial life, and simulation experiments using an AChem system. Biological experiments have shown that terrestrial life possesses a PSD mechanism as an endergonic, genetically regulated process and that hydrolysis, which decomposes a BP into BMs, is one of the main processes of such a mechanism. In simulation experiments, we compared different virtual self-decomposition processes. The virtual species in which the self-decomposition process mainly involved covalent bond cleavage from a BP to BMs showed evolutionary superiority over other species in which the self-decomposition process involved cleavage from BP to classes lower than BM. These converging findings strongly support the existence of PSD and the validity and effectiveness of the HBCB model.

Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

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Cornelia Meinert

2010-05-01

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

Integration of biomolecular logic gates with field-effect transducers

Energy Technology Data Exchange (ETDEWEB)

Poghossian, A., E-mail: a.poghossian@fz-juelich.de [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Malzahn, K. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Abouzar, M.H. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Mehndiratta, P. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Katz, E. [Department of Chemistry and Biomolecular Science, NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, NY 13699-5810 (United States); Schoening, M.J. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany)

2011-11-01

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-SiO{sub 2}-Ta{sub 2}O{sub 5} 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 (Ta{sub 2}O{sub 5}) 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.

Integration of biomolecular logic gates with field-effect transducers

International Nuclear Information System (INIS)

Poghossian, A.; Malzahn, K.; Abouzar, M.H.; Mehndiratta, P.; Katz, E.; Schoening, M.J.

2011-01-01

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-SiO 2 -Ta 2 O 5 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 (Ta 2 O 5 ) 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.

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.

Single-molecule imaging and manipulation of biomolecular machines and systems.

Science.gov (United States)

Iino, Ryota; Iida, Tatsuya; Nakamura, Akihiko; Saita, Ei-Ichiro; You, Huijuan; Sako, Yasushi

2018-02-01

Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Science.gov (United States)

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

2014-11-04

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

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

International Nuclear Information System (INIS)

Lee, In-Hee; Yang, Kyung-Ae; Zhang, Byoung-Tak; Lee, Ji-Hoon; Park, Ji-Yoon; Chai, Young Gyu; Lee, Jae-Hoon

2008-01-01

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

Affinity Capillary Electrophoresis – A Powerful Tool to Investigate Biomolecular Interactions

Czech Academy of Sciences Publication Activity Database

Kašička, Václav

2017-01-01

Roč. 30, č. 5 (2017), s. 248 ISSN 1471-6577 Institutional support: RVO:61388963 Keywords : capillary affinity electrophoresis * biomolecular interactions * binding constants Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 0.663, year: 2016

DNA-assisted swarm control in a biomolecular motor system.

Science.gov (United States)

Keya, Jakia Jannat; Suzuki, Ryuhei; Kabir, Arif Md Rashedul; Inoue, Daisuke; Asanuma, Hiroyuki; Sada, Kazuki; Hess, Henry; Kuzuya, Akinori; Kakugo, Akira

2018-01-31

In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.

In situ, accurate, surface-enhanced Raman scattering detection of cancer cell nucleus with synchronous location by an alkyne-labeled biomolecular probe.

Science.gov (United States)

Zhang, Jing; Liang, Lijia; Guan, Xin; Deng, Rong; Qu, Huixin; Huang, Dianshuai; Xu, Shuping; Liang, Chongyang; Xu, Weiqing

2018-01-01

A surface-enhanced Raman scattering (SERS) method for in situ detection and analysis of the intranuclear biomolecular information of a cell has been developed based on a small, biocompatible, nuclear-targeting alkyne-tagged deoxyribonucleic acid (DNA) probe (5-ethynyl-2'-deoxyuridine, EDU) that can specially accumulate in the cell nucleus during DNA replications to precisely locate the nuclear region without disturbance in cell biological activities and functions. Since the specific alkyne group shows a Raman peak in the Raman-silent region of cells, it is an interior label to visualize the nuclear location synchronously in real time when measuring the SERS spectra of a cell. Because no fluorescent-labeled dyes were used for locating cell nuclei, this method is simple, nondestructive, non- photobleaching, and valuable for the in situ exploration of vital physiological processes with DNA participation in cell organelles. Graphical abstract A universal strategy was developed to accurately locate the nuclear region and obtain precise molecular information of cell nuclei by SERS.

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

Science.gov (United States)

2017-01-01

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/ PMID:28749969

Foreword [IJEGMBE 2015: India-Japan expert group meeting on biomolecular electronics and organic nanotechnology for environment preservation, Fukuoka (Japan), 23-26 December 2015

International Nuclear Information System (INIS)

2016-01-01

There is increased interest in organic nanotechnology and biomolecular electronics for environmental preservation, and in their anticipated impact on the economics of both the developing and the developed world. Keeping this in mind, the Department of Biological Functions, Graduate School of Life Sciences and Systems Engineering, Kyushu Institute of Technology (KIT), Kitakyushu, Japan, and the Department of Science and Technology Centre on Biomolecular Electronics (DSTCBE), National Physical Laboratory (NPL) jointly organized the India-Japan Workshop on Biomolecular Electronics and Organic Nanotechnology for Environmental Preservation (IJWBME 2009) at NPL, New Delhi from 17 th - 19 th December 2009, IJWBME 2011 at EGRET Himeji, Himeji, from 7 th - 10 th December, Japan, and IJWBME 2013 at Delhi Technological University, New Delhi, from 13 th - 15 th December. The India-Japan Expert Group Meeting on Biomolecular Electronics and Organic Nanotechnology for Environment Preservation (IJEGMBE) will be held from 22 th – 25 th , December, 2015, at Nakamura Centenary Memorial Hall, Kyushu Institute of Technology, Kitakyushu, Japan in association with Delhi Technological University, Delhi, India. Recent years have seen rapid growth in the area of Biomolecular Electronics involving the association and expertise of physicists, biologists, chemists, electronics engineers and information technologists. There is increasing interest in the development of nanotechnology and biomolecular electronic devices for the preservation of our precious environment. In this context, the world of the electronics, which developed on Si semiconductors, is going to change drastically. A paradigm shift towards organic or printed electronics is more likely in the future. The field of organic electronics promises exciting new technologies based on inexpensive and mechanically flexible electronic devices, and is now starting to see commercial success. On the sidelines of this increasingly well

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…

Multiscale Persistent Functions for Biomolecular Structure Characterization

Energy Technology Data Exchange (ETDEWEB)

Xia, Kelin [Nanyang Technological University (Singapore). Division of Mathematical Sciences, School of Physical, Mathematical Sciences and School of Biological Sciences; Li, Zhiming [Central China Normal University, Wuhan (China). Key Laboratory of Quark and Lepton Physics (MOE) and Institute of Particle Physics; Mu, Lin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division

2017-11-02

Here in this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. Additionally, it is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first

Scanning probe and optical tweezer investigations of biomolecular interactions

International Nuclear Information System (INIS)

Rigby-Singleton, Shellie

2002-01-01

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 ∼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 have

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.

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.

Application of biomolecular recognition via magnetic nanoparticle in nanobiotechnology

Science.gov (United States)

Shen, Wei-Zheng; Cetinel, Sibel; Montemagno, Carlo

2018-05-01

The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.

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.

Synthetic Approach to biomolecular science by cyborg supramolecular chemistry.

Science.gov (United States)

Kurihara, Kensuke; Matsuo, Muneyuki; Yamaguchi, Takumi; Sato, Sota

2018-02-01

To imitate the essence of living systems via synthetic chemistry approaches has been attempted. With the progress in supramolecular chemistry, it has become possible to synthesize molecules of a size and complexity close to those of biomacromolecules. Recently, the combination of precisely designed supramolecules with biomolecules has generated structural platforms for designing and creating unique molecular systems. Bridging between synthetic chemistry and biomolecular science is also developing methodologies for the creation of artificial cellular systems. This paper provides an overview of the recently expanding interdisciplinary research to fuse artificial molecules with biomolecules, that can deepen our understanding of the dynamical ordering of biomolecules. Using bottom-up approaches based on the precise chemical design, synthesis and hybridization of artificial molecules with biological materials have been realizing the construction of sophisticated platforms having the fundamental functions of living systems. The effective hybrid, molecular cyborg, approaches enable not only the establishment of dynamic systems mimicking nature and thus well-defined models for biophysical understanding, but also the creation of those with highly advanced, integrated functions. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

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)

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

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

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.

Synergy of Two Highly Specific Biomolecular Recognition Events

DEFF Research Database (Denmark)

Ejlersen, Maria; Christensen, Niels Johan; Sørensen, Kasper K

2018-01-01

Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino......-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA...

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.

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.

Biomolecular solid state NMR with magic-angle spinning at 25K.

Science.gov (United States)

Thurber, Kent R; Tycko, Robert

2008-12-01

A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.

Integrative NMR for biomolecular research

International Nuclear Information System (INIS)

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

2016-01-01

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 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 http://pine.nmrfam.wisc.edu/integrative.html ).

Integrative NMR for biomolecular research

Energy Technology Data Exchange (ETDEWEB)

Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

2016-04-15

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 http://pine.nmrfam.wisc.edu/download{sub p}ackages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

REVIEW ARTICLE: How do biomolecular systems speed up and regulate rates?

Science.gov (United States)

Zhou, Huan-Xiang

2005-09-01

The viability of a biological system depends upon careful regulation of the rates of various processes. These rates have limits imposed by intrinsic chemical or physical steps (e.g., diffusion). These limits can be expanded by interactions and dynamics of the biomolecules. For example, (a) a chemical reaction is catalyzed when its transition state is preferentially bound to an enzyme; (b) the folding of a protein molecule is speeded up by specific interactions within the transition-state ensemble and may be assisted by molecular chaperones; (c) the rate of specific binding of a protein molecule to a cellular target can be enhanced by mechanisms such as long-range electrostatic interactions, nonspecific binding and folding upon binding; (d) directional movement of motor proteins is generated by capturing favorable Brownian motion through intermolecular binding energy; and (e) conduction and selectivity of ions through membrane channels are controlled by interactions and the dynamics of channel proteins. Simple physical models are presented here to illustrate these processes and provide a unifying framework for understanding speed attainment and regulation in biomolecular systems.

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

KAUST Repository

Sobhy, M. A.; Elshenawy, M. M.; Takahashi, Masateru; Whitman, B. H.; Walter, N. G.; Hamdan, S. M.

2011-01-01

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

Electrostatics in biomolecular simulations : where are we now and where are we heading?

NARCIS (Netherlands)

Karttunen, M.E.J.; Rottler, J.; Vattulainen, I.; Sagui, C.

2008-01-01

Chapter 2. In this review, we discuss current methods and developments in the treatment of electrostatic interactions in biomolecular and soft matter simulations. We review the current ‘work horses’, namely, Ewald summation based methods such the Particle-Mesh Ewald, and others, and also newer

A compact imaging spectroscopic system for biomolecular detections on plasmonic chips.

Science.gov (United States)

Lo, Shu-Cheng; Lin, En-Hung; Wei, Pei-Kuen; Tsai, Wan-Shao

2016-10-17

In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings. The detected sensitivities of the plasmonic chip are comparable with a commercial spectrometer. An extra one-dimensional scanning stage enables high-throughput detection of protein binding on a designed plasmonic chip consisting of several nanoslit arrays with different periods. The detected resonance wavelengths match well with the grating equation under an air environment. Wavelength shifts between 1 and 9 nm are detected for antigens of various concentrations binding with antibodies. A simple, mass-productive and cost-effective method has been demonstrated on the imaging spectroscopic system for real-time, label-free, highly sensitive and high-throughput screening of biomolecular interactions.

Writing, Proofreading and Editing in Information Theory

Directory of Open Access Journals (Sweden)

J. Ricardo Arias-Gonzalez

2018-05-01

Full Text Available Information is a physical entity amenable to be described by an abstract theory. The concepts associated with the creation and post-processing of the information have not, however, been mathematically established, despite being broadly used in many fields of knowledge. Here, inspired by how information is managed in biomolecular systems, we introduce writing, entailing any bit string generation, and revision, as comprising proofreading and editing, in information chains. Our formalism expands the thermodynamic analysis of stochastic chains made up of material subunits to abstract strings of symbols. We introduce a non-Markovian treatment of operational rules over the symbols of the chain that parallels the physical interactions responsible for memory effects in material chains. Our theory underlies any communication system, ranging from human languages and computer science to gene evolution.

Rapid prototyping of nanofluidic systems using size-reduced electrospun nanofibers for biomolecular analysis.

Science.gov (United States)

Park, Seung-Min; Huh, Yun Suk; Szeto, Kylan; Joe, Daniel J; Kameoka, Jun; Coates, Geoffrey W; Edel, Joshua B; Erickson, David; Craighead, Harold G

2010-11-05

Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.

Biomolecular ions in superfluid helium nanodroplets

Energy Technology Data Exchange (ETDEWEB)

Gonzalez Florez, Ana Isabel

2016-07-01

The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

Biomolecular ions in superfluid helium nanodroplets

International Nuclear Information System (INIS)

Gonzalez Florez, Ana Isabel

2016-01-01

The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

A hydrogel-based versatile screening platform for specific biomolecular recognition in a well plate format.

Science.gov (United States)

Beer, Meike V; Rech, Claudia; Diederichs, Sylvia; Hahn, Kathrin; Bruellhoff, Kristina; Möller, Martin; Elling, Lothar; Groll, Jürgen

2012-04-01

Precise determination of biomolecular interactions in high throughput crucially depends on a surface coating technique that allows immobilization of a variety of interaction partners in a non-interacting environment. We present a one-step hydrogel coating system based on isocyanate functional six-arm poly(ethylene oxide)-based star polymers for commercially available 96-well microtiter plates that combines a straightforward and robust coating application with versatile bio-functionalization. This system generates resistance to unspecific protein adsorption and cell adhesion, as demonstrated with fluorescently labeled bovine serum albumin and primary human dermal fibroblasts (HDF), and high specificity for the assessment of biomolecular recognition processes when ligands are immobilized on this surface. One particular advantage is the wide range of biomolecules that can be immobilized and convert the per se inert coating into a specifically interacting surface. We here demonstrate the immobilization and quantification of a broad range of biochemically important ligands, such as peptide sequences GRGDS and GRGDSK-biotin, the broadly applicable coupler molecule biocytin, the protein fibronectin, and the carbohydrates N-acetylglucosamine and N-acetyllactosamine. A simplified protocol for an enzyme-linked immunosorbent assay was established for the detection and quantification of ligands on the coating surface. Cell adhesion on the peptide and protein-modified surfaces was assessed using HDF. All coatings were applied using a one-step preparation technique, including bioactivation, which makes the system suitable for high-throughput screening in a format that is compatible with the most routinely used testing systems.

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

Science.gov (United States)

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

2016-08-10

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

Instrumental biosensors: new perspectives for the analysis of biomolecular interactions.

Science.gov (United States)

Nice, E C; Catimel, B

1999-04-01

The use of instrumental biosensors in basic research to measure biomolecular interactions in real time is increasing exponentially. Applications include protein-protein, protein-peptide, DNA-protein, DNA-DNA, and lipid-protein interactions. Such techniques have been applied to, for example, antibody-antigen, receptor-ligand, signal transduction, and nuclear receptor studies. This review outlines the principles of two of the most commonly used instruments and highlights specific operating parameters that will assist in optimising experimental design, data generation, and analysis.

NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

Science.gov (United States)

Sekhar, Ashok; Kay, Lewis E

2013-08-06

The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

Spatio-temporal bio-radical processes: the state of the art and new challenges

International Nuclear Information System (INIS)

Gauduel, Y.A.

2013-01-01

The course of ultrafast elementary bio-molecular damage governed by low energy electrons can be carefully investigated in the pre-thermal regime. During this specific regime, the energy of partially localized electron is still higher than the thermal energy kT (0.025 eV) but its interaction potential with molecules is directly dependent on the state density fluctuations of the environment. In presence of water molecules two well-defined non-equilibrium low-energy electron configurations, 2p-like excited pre-hydrated electron and electron-radical pair, represent very interesting quantum entities for the real-time investigation of their interactions with bio-molecular environments. In the framework of nonadiabatic trajectories, quantum branching ratios of low energy electron pathways are highly influenced by time-dependent water caging effects. The investigation of ultrafast concerted processes with low energy localized electrons contributes to the concept of tenuous borderline between direct and indirect molecular damage at the local order. The quantum character of very-short lived low-energy electron in a pre-hydrated configuration (infrared 2p-like excited electron) provides a unique sub-nano-metric probe to spatially explore early radiation damage on biologically relevant molecules. For the first time, femto-bio-radical investigations performed in aqueous environments give correlated spatial and temporal information on bio-molecular damage triggered by ultrafast low energy electron attachments. In the future, this innovative approach would be applied to more complex bio-molecular architectures such as DNA or protein complexes

Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions.

Science.gov (United States)

Lu, Benzhuo; Holst, Michael J; McCammon, J Andrew; Zhou, Y C

2010-09-20

In this paper we developed accurate finite element methods for solving 3-D Poisson-Nernst-Planck (PNP) equations with singular permanent charges for electrodiffusion in solvated biomolecular systems. The electrostatic Poisson equation was defined in the biomolecules and in the solvent, while the Nernst-Planck equation was defined only in the solvent. We applied a stable regularization scheme to remove the singular component of the electrostatic potential induced by the permanent charges inside biomolecules, and formulated regular, well-posed PNP equations. An inexact-Newton method was used to solve the coupled nonlinear elliptic equations for the steady problems; while an Adams-Bashforth-Crank-Nicolson method was devised for time integration for the unsteady electrodiffusion. We numerically investigated the conditioning of the stiffness matrices for the finite element approximations of the two formulations of the Nernst-Planck equation, and theoretically proved that the transformed formulation is always associated with an ill-conditioned stiffness matrix. We also studied the electroneutrality of the solution and its relation with the boundary conditions on the molecular surface, and concluded that a large net charge concentration is always present near the molecular surface due to the presence of multiple species of charged particles in the solution. The numerical methods are shown to be accurate and stable by various test problems, and are applicable to real large-scale biophysical electrodiffusion problems.

Perspectives of biomolecular NMR in drug discovery: the blessing and curse of versatility

International Nuclear Information System (INIS)

Jahnke, Wolfgang

2007-01-01

The versatility of NMR and its broad applicability to several stages in the drug discovery process is well known and generally considered one of the major strengths of NMR (Pellecchia et al., Nature Rev Drug Discov 1:211-219, 2002; Stockman and Dalvit, Prog Nucl Magn Reson Spectrosc 41:187-231, 2002; Lepre et al., Comb Chem High throughput screen 5:583-590, 2002; Wyss et al., Curr Opin Drug Discov Devel 5:630-647, 2002; Jahnke and Widmer, Cell Mol Life Sci 61:580-599, 2004; Huth et al., Methods Enzymol 394:549-571, 2005b; Klages et al., Mol Biosyst 2:318-332, 2006; Takeuchi and Wagner, Curr Opin Struct Biol 16:109-117, 2006; Zartler and Shapiro, Curr Pharm Des 12:3963-3972, 2006). Indeed, NMR is the only biophysical technique which can detect and quantify molecular interactions, and at the same time provide detailed structural information with atomic level resolution. NMR should therefore be ideally suited and widely requested as a tool for drug discovery research, and numerous examples of drug discovery projects which have substantially benefited from NMR contributions or were even driven by NMR have been described in the literature. However, not all pharmaceutical companies have rigorously implemented NMR as integral tool of their research processes. Some companies invest with limited resources, and others do not use biomolecular NMR at all. This discrepancy in assessing the value of a technology is striking, and calls for clarification-under which circumstances can NMR provide added value to the drug discovery process? What kind of contributions can NMR make, and how is it implemented and integrated for maximum impact? This perspectives article suggests key areas of impact for NMR, and a model of integrating NMR with other technologies to realize synergies and maximize their value for drug discovery

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

Cancer genetics meets biomolecular mechanism-bridging an age-old gulf.

Science.gov (United States)

González-Sánchez, Juan Carlos; Raimondi, Francesco; Russell, Robert B

2018-02-01

Increasingly available genomic sequencing data are exploited to identify genes and variants contributing to diseases, particularly cancer. Traditionally, methods to find such variants have relied heavily on allele frequency and/or familial history, often neglecting to consider any mechanistic understanding of their functional consequences. Thus, while the set of known cancer-related genes has increased, for many, their mechanistic role in the disease is not completely understood. This issue highlights a wide gap between the disciplines of genetics, which largely aims to correlate genetic events with phenotype, and molecular biology, which ultimately aims at a mechanistic understanding of biological processes. Fortunately, new methods and several systematic studies have proved illuminating for many disease genes and variants by integrating sequencing with mechanistic data, including biomolecular structures and interactions. These have provided new interpretations for known mutations and suggested new disease-relevant variants and genes. Here, we review these approaches and discuss particular examples where these have had a profound impact on the understanding of human cancers. © 2018 Federation of European Biochemical Societies.

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

Science.gov (United States)

Goni, Md Osman

2013-01-01

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

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

Science.gov (United States)

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

A new strategy for imaging biomolecular events through interactions between liquid crystals and oil-in-water emulsions.

Science.gov (United States)

Hu, Qiong-Zheng; Jang, Chang-Hyun

2012-11-21

In this study, we demonstrate a new strategy to image biomolecular events through interactions between liquid crystals (LCs) and oil-in-water emulsions. The optical response had a dark appearance when a nematic LC, 4-cyano-4'-pentylbiphenyl (5CB), is in contact with emulsion droplets of glyceryl trioleate (GT). In contrast, the optical response had a bright appearance when 5CB is in contact with GT emulsions decorated with surfactants such as sodium oleate. Since lipase can hydrolyze GT and produce oleic acid, the optical response also displays a bright appearance after 5CB has been in contact with a mixture of lipase and GT emulsions. These results indicate the feasibility of monitoring biomolecular events through interactions between LCs and oil-in-water emulsions.

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. Copyright © 2015 Elsevier Inc. All rights reserved.

Proceedings of the international advisory committee on 'biomolecular dynamics instrument DNA' and the workshop on 'biomolecular dynamics backscattering spectrometers'

International Nuclear Information System (INIS)

Arai, Masatoshi; Aizawa, Kazuya; Nakajima, Kenji; Shibata, Kaoru; Takahashi, Nobuaki

2008-08-01

A workshop entitled 'Biomolecular Dynamics Backscattering Spectrometers' was held on February 27th - 29th, 2008 at J-PARC Center, Japan Atomic Energy Agency. This workshop was planned to be held for aiming to realize an innovative neutron backscattering instrument, namely DNA, in the MLF and thus four leading scientists in the field of neutron backscattering instruments were invited as the International Advisory Committee (IAC member: Dr. Dan Neumann (Chair); Prof. Ferenc Mezei; Dr. Hannu Mutka; Dr. Philip Tregenna-Piggott) for DNA from institutes in the United States, France and Switzerland, where backscattering instruments are in-service. It was therefore held in the form of lecture anterior and then in the form of the committee posterior. This report includes the executive summary of the IAC and materials of the presentations in the IAC and the workshop. (author)

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

International Nuclear Information System (INIS)

Manil, B.

2007-11-01

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)

Quantum Information Processing

CERN Document Server

Leuchs, Gerd

2005-01-01

Quantum processing and communication is emerging as a challenging technique at the beginning of the new millennium. This is an up-to-date insight into the current research of quantum superposition, entanglement, and the quantum measurement process - the key ingredients of quantum information processing. The authors further address quantum protocols and algorithms. Complementary to similar programmes in other countries and at the European level, the German Research Foundation (DFG) started a focused research program on quantum information in 1999. The contributions - written by leading experts - bring together the latest results in quantum information as well as addressing all the relevant questions

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.

Conceptual models of information processing

Science.gov (United States)

Stewart, L. J.

1983-01-01

The conceptual information processing issues are examined. Human information processing is defined as an active cognitive process that is analogous to a system. It is the flow and transformation of information within a human. The human is viewed as an active information seeker who is constantly receiving, processing, and acting upon the surrounding environmental stimuli. Human information processing models are conceptual representations of cognitive behaviors. Models of information processing are useful in representing the different theoretical positions and in attempting to define the limits and capabilities of human memory. It is concluded that an understanding of conceptual human information processing models and their applications to systems design leads to a better human factors approach.

Towards sensitive, high-throughput, biomolecular assays based on fluorescence lifetime

Science.gov (United States)

Ioanna Skilitsi, Anastasia; Turko, Timothé; Cianfarani, Damien; Barre, Sophie; Uhring, Wilfried; Hassiepen, Ulrich; Léonard, Jérémie

2017-09-01

Time-resolved fluorescence detection for robust sensing of biomolecular interactions is developed by implementing time-correlated single photon counting in high-throughput conditions. Droplet microfluidics is used as a promising platform for the very fast handling of low-volume samples. We illustrate the potential of this very sensitive and cost-effective technology in the context of an enzymatic activity assay based on fluorescently-labeled biomolecules. Fluorescence lifetime detection by time-correlated single photon counting is shown to enable reliable discrimination between positive and negative control samples at a throughput as high as several hundred samples per second.

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

A variational approach to moment-closure approximations for the kinetics of biomolecular reaction networks

Science.gov (United States)

Bronstein, Leo; Koeppl, Heinz

2018-01-01

Approximate solutions of the chemical master equation and the chemical Fokker-Planck equation are an important tool in the analysis of biomolecular reaction networks. Previous studies have highlighted a number of problems with the moment-closure approach used to obtain such approximations, calling it an ad hoc method. In this article, we give a new variational derivation of moment-closure equations which provides us with an intuitive understanding of their properties and failure modes and allows us to correct some of these problems. We use mixtures of product-Poisson distributions to obtain a flexible parametric family which solves the commonly observed problem of divergences at low system sizes. We also extend the recently introduced entropic matching approach to arbitrary ansatz distributions and Markov processes, demonstrating that it is a special case of variational moment closure. This provides us with a particularly principled approximation method. Finally, we extend the above approaches to cover the approximation of multi-time joint distributions, resulting in a viable alternative to process-level approximations which are often intractable.

Perspective: Markov models for long-timescale biomolecular dynamics

International Nuclear Information System (INIS)

Schwantes, C. R.; McGibbon, R. T.; Pande, V. 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

Perspective: Markov models for long-timescale biomolecular dynamics

Energy Technology Data Exchange (ETDEWEB)

Schwantes, C. R.; McGibbon, R. T. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Pande, V. S., E-mail: pande@stanford.edu [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Department of Computer Science, Stanford University, Stanford, California 94305 (United States); Department of Structural Biology, Stanford University, Stanford, California 94305 (United States); Biophysics Program, Stanford University, Stanford, California 94305 (United States)

2014-09-07

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.

Techniques of biomolecular quantification through AMS detection of radiocarbon

International Nuclear Information System (INIS)

Vogel, S.J.; Turteltaub, K.W.; Frantz, C.; Felton, J.S.; Gledhill, B.L.

1992-01-01

Accelerator mass spectrometry offers a large gain over scintillation counting in sensitivity for detecting radiocarbon in biomolecular tracing. Application of this sensitivity requires new considerations of procedures to extract or isolate the carbon fraction to be quantified, to inventory all carbon in the sample, to prepare graphite from the sample for use in the spectrometer, and to derive a meaningful quantification from the measured isotope ratio. These procedures need to be accomplished without contaminating the sample with radiocarbon, which may be ubiquitous in laboratories and on equipment previously used for higher dose, scintillation experiments. Disposable equipment, materials and surfaces are used to control these contaminations. Quantification of attomole amounts of labeled substances are possible through these techniques

Pre-Clinical Tests of an Integrated CMOS Biomolecular Sensor for Cardiac Diseases Diagnosis.

Science.gov (United States)

Lee, Jen-Kuang; Wang, I-Shun; Huang, Chi-Hsien; Chen, Yih-Fan; Huang, Nien-Tsu; Lin, Chih-Ting

2017-11-26

Coronary artery disease and its related complications pose great threats to human health. In this work, we aim to clinically evaluate a CMOS field-effect biomolecular sensor for cardiac biomarkers, cardiac-specific troponin-I (cTnI), N -terminal prohormone brain natriuretic peptide (NT-proBNP), and interleukin-6 (IL-6). The CMOS biosensor is implemented via a standard commercialized 0.35 μm CMOS process. To validate the sensing characteristics, in buffer conditions, the developed CMOS biosensor has identified the detection limits of IL-6, cTnI, and NT-proBNP as being 45 pM, 32 pM, and 32 pM, respectively. In clinical serum conditions, furthermore, the developed CMOS biosensor performs a good correlation with an enzyme-linked immuno-sorbent assay (ELISA) obtained from a hospital central laboratory. Based on this work, the CMOS field-effect biosensor poses good potential for accomplishing the needs of a point-of-care testing (POCT) system for heart disease diagnosis.

ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.

Science.gov (United States)

Wood, Christopher W; Heal, Jack W; Thomson, Andrew R; Bartlett, Gail J; Ibarra, Amaurys Á; Brady, R Leo; Sessions, Richard B; Woolfson, Derek N

2017-10-01

The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the 'dark matter of protein-fold space'. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. d.n.woolfson@bristol.ac.uk or chris.wood@bristol.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

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.

Evolution of biomolecular loadings along a major river system

Science.gov (United States)

Freymond, Chantal V.; Kündig, Nicole; Stark, Courcelle; Peterse, Francien; Buggle, Björn; Lupker, Maarten; Plötze, Michael; Blattmann, Thomas M.; Filip, Florin; Giosan, Liviu; Eglinton, Timothy I.

2018-02-01

Understanding the transport history and fate of organic carbon (OC) within river systems is crucial in order to constrain the dynamics and significance of land-ocean interactions as a component of the global carbon cycle. Fluvial export and burial of terrestrial OC in marine sediments influences atmospheric CO2 over a range of timescales, while river-dominated sedimentary sequences can provide valuable archives of paleoenvironmental information. While there is abundant evidence that the association of organic matter (OM) with minerals exerts an important influence on its stability as well as hydrodynamic behavior in aquatic systems, there is a paucity of information on where such associations form and how they evolve during fluvial transport. Here, we track total organic carbon (TOC) and terrestrial biomarker concentrations (plant wax-derived long-chain fatty acids (FA), branched glycerol dialkyl glycerol tetraethers (brGDGTs) and lignin-derived phenols) in sediments collected along the entire course of the Danube River system in the context of sedimentological parameters. Mineral-specific surface area-normalized biomarker and TOC concentrations show a systematic decrease from the upper to the lower Danube basin. Changes in OM loading of the available mineral phase correspond to a net decrease of 70-80% of different biomolecular components. Ranges for biomarker loadings on Danube River sediments, corresponding to 0.4-1.5 μgFA/m2 for long-chain (n-C24-32) fatty acids and 17-71 ngbrGDGT/m2 for brGDGTs, are proposed as a benchmark for comparison with other systems. We propose that normalizing TOC as well as biomarker concentrations to mineral surface area provides valuable quantitative constraints on OM dynamics and organo-mineral interactions during fluvial transport from terrigenous source to oceanic sink.

Continuous-variable quantum information processing

DEFF Research Database (Denmark)

Andersen, Ulrik Lund; Leuchs, G.; Silberhorn, C.

2010-01-01

the continuous degree of freedom of a quantum system for encoding, processing or detecting information, one enters the field of continuous-variable (CV) quantum information processing. In this paper we review the basic principles of CV quantum information processing with main focus on recent developments...... in the field. We will be addressing the three main stages of a quantum information system; the preparation stage where quantum information is encoded into CVs of coherent states and single-photon states, the processing stage where CV information is manipulated to carry out a specified protocol and a detection...... stage where CV information is measured using homodyne detection or photon counting....

Orientation of biomolecular assemblies in a microfluidic jet

International Nuclear Information System (INIS)

Priebe, M; Kalbfleisch, S; Tolkiehn, M; Salditt, T; Koester, S; Abel, B; Davies, R J

2010-01-01

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

ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

Science.gov (United States)

Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

2018-05-08

Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Methods of information processing

Energy Technology Data Exchange (ETDEWEB)

Kosarev, Yu G; Gusev, V D

1978-01-01

Works are presented on automation systems for editing and publishing operations by methods of processing symbol information and information contained in training selection (ranking of objectives by promise, classification algorithm of tones and noise). The book will be of interest to specialists in the automation of processing textural information, programming, and pattern recognition.

Introduction to a Protein Interaction System Used for Quantitative Evaluation of Biomolecular Interactions

OpenAIRE

Yamniuk, Aaron

2013-01-01

A central goal of molecular biology is the determination of biomolecular function. This comes largely from a knowledge of the non-covalent interactions that biological small and macro-molecules experience. The fundamental mission of the Molecular Interactions Research Group (MIRG) of the ABRF is to show how solution biophysical tools are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core t...

Natural Information Processing Systems

OpenAIRE

John Sweller; Susan Sweller

2006-01-01

Natural information processing systems such as biological evolution and human cognition organize information used to govern the activities of natural entities. When dealing with biologically secondary information, these systems can be specified by five common principles that we propose underlie natural information processing systems. The principles equate: (1) human long-term memory with a genome; (2) learning from other humans with biological reproduction; (3) problem solving through random ...

Thermodynamic framework for information in nanoscale systems with memory.

Science.gov (United States)

Arias-Gonzalez, J Ricardo

2017-11-28

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.

Thermodynamic framework for information in nanoscale systems with memory

Science.gov (United States)

Arias-Gonzalez, J. Ricardo

2017-11-01

Information is represented by linear strings of symbols with memory that carry errors as a result of their stochastic nature. Proofreading and edition are assumed to improve certainty although such processes may not be effective. Here, we develop a thermodynamic theory for material chains made up of nanoscopic subunits with symbolic meaning in the presence of memory. This framework is based on the characterization of single sequences of symbols constructed under a protocol and is used to derive the behavior of ensembles of sequences similarly constructed. We then analyze the role of proofreading and edition in the presence of memory finding conditions to make revision an effective process, namely, to decrease the entropy of the chain. Finally, we apply our formalism to DNA replication and RNA transcription finding that Watson and Crick hybridization energies with which nucleotides are branched to the template strand during the copying process are optimal to regulate the fidelity in proofreading. These results are important in applications of information theory to a variety of solid-state physical systems and other biomolecular processes.

Information processing, computation, and cognition.

Science.gov (United States)

Piccinini, Gualtiero; Scarantino, Andrea

2011-01-01

Computation and information processing are among the most fundamental notions in cognitive science. They are also among the most imprecisely discussed. Many cognitive scientists take it for granted that cognition involves computation, information processing, or both - although others disagree vehemently. Yet different cognitive scientists use 'computation' and 'information processing' to mean different things, sometimes without realizing that they do. In addition, computation and information processing are surrounded by several myths; first and foremost, that they are the same thing. In this paper, we address this unsatisfactory state of affairs by presenting a general and theory-neutral account of computation and information processing. We also apply our framework by analyzing the relations between computation and information processing on one hand and classicism, connectionism, and computational neuroscience on the other. We defend the relevance to cognitive science of both computation, at least in a generic sense, and information processing, in three important senses of the term. Our account advances several foundational debates in cognitive science by untangling some of their conceptual knots in a theory-neutral way. By leveling the playing field, we pave the way for the future resolution of the debates' empirical aspects.

Native fluorescence detection of biomolecular and pharmaceutical compounds in capillary electrophoresis: detector designs, performance and applications: A review

NARCIS (Netherlands)

de Kort, B.J.; de Jong, G.J.; Somsen, G.W.

2013-01-01

This review treats the coupling of capillary electrophoresis (CE) with fluorescence detection (Flu) for the analysis of natively fluorescent biomolecular and pharmaceutical compounds. CE-Flu combines the excellent separation efficiency of CE with the high selectivity and sensitivity of Flu. In

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

Directory of Open Access Journals (Sweden)

S. Iachettini

2015-10-01

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

Hybrid organic semiconductor lasers for bio-molecular sensing.

Science.gov (United States)

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

2014-01-01

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

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.

Scientific information processing procedures

Directory of Open Access Journals (Sweden)

García, Maylin

2013-07-01

Full Text Available The paper systematizes several theoretical view-points on scientific information processing skill. It decomposes the processing skills into sub-skills. Several methods such analysis, synthesis, induction, deduction, document analysis were used to build up a theoretical framework. Interviews and survey to professional being trained and a case study was carried out to evaluate the results. All professional in the sample improved their performance in scientific information processing.

Information accessibility and cryptic processes

Energy Technology Data Exchange (ETDEWEB)

Mahoney, John R; Ellison, Christopher J; Crutchfield, James P [Complexity Sciences Center and Physics Department, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States)], E-mail: jrmahoney@ucdavis.edu, E-mail: cellison@cse.ucdavis.edu, E-mail: chaos@cse.ucdavis.edu

2009-09-11

We give a systematic expansion of the crypticity-a recently introduced measure of the inaccessibility of a stationary process's internal state information. This leads to a hierarchy of k-cryptic processes and allows us to identify finite-state processes that have infinite cryptic order-the internal state information is present across arbitrarily long, observed sequences. The crypticity expansion is exact in both the finite- and infinite-order cases. It turns out that k-crypticity is complementary to the Markovian finite-order property that describes state information in processes. One application of these results is an efficient expansion of the excess entropy-the mutual information between a process's infinite past and infinite future-that is finite and exact for finite-order cryptic processes. (fast track communication)

Motivated information processing and group decision-making : Effects of process accountability on information processing and decision quality

NARCIS (Netherlands)

Scholten, Lotte; van Knippenberg, Daan; Nijstad, Bernard A.; De Dreu, Carsten K. W.

Integrating dual-process models [Chaiken, S., & Trope, Y. (Eds.). (1999). Dual-process theories in social psychology. NewYork: Guilford Press] with work on information sharing and group decision-making [Stasser, G., & Titus, W. (1985). Pooling of unshared information in group decision making: biased

Biochemical Stability Analysis of Nano Scaled Contrast Agents Used in Biomolecular Imaging Detection of Tumor Cells

Science.gov (United States)

Kim, Jennifer; Kyung, Richard

Imaging contrast agents are materials used to improve the visibility of internal body structures in the imaging process. Many agents that are used for contrast enhancement are now studied empirically and computationally by researchers. Among various imaging techniques, magnetic resonance imaging (MRI) has become a major diagnostic tool in many clinical specialties due to its non-invasive characteristic and its safeness in regards to ionizing radiation exposure. Recently, researchers have prepared aqueous fullerene nanoparticles using electrochemical methods. In this paper, computational simulations of thermodynamic stabilities of nano scaled contrast agents that can be used in biomolecular imaging detection of tumor cells are presented using nanomaterials such as fluorescent functionalized fullerenes. In addition, the stability and safety of different types of contrast agents composed of metal oxide a, b, and c are tested in the imaging process. Through analysis of the computational simulations, the stabilities of the contrast agents, determined by optimized energies of the conformations, are presented. The resulting numerical data are compared. In addition, Density Functional Theory (DFT) is used in order to model the electron properties of the compound.

Information Processing and Limited Liability

OpenAIRE

Bartosz Mackowiak; Mirko Wiederholt

2012-01-01

Decision-makers often face limited liability and thus know that their loss will be bounded. We study how limited liability affects the behavior of an agent who chooses how much information to acquire and process in order to take a good decision. We find that an agent facing limited liability processes less information than an agent with unlimited liability. The informational gap between the two agents is larger in bad times than in good times and when information is more costly to process.

THz time domain spectroscopy of biomolecular conformational modes

International Nuclear Information System (INIS)

Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

2002-01-01

We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm -1 range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules

Protein-Ligand Informatics Force Field (PLIff): Toward a Fully Knowledge Driven "Force Field" for Biomolecular Interactions.

Science.gov (United States)

Verdonk, Marcel L; Ludlow, R Frederick; Giangreco, Ilenia; Rathi, Prakash Chandra

2016-07-28

The Protein Data Bank (PDB) contains a wealth of data on nonbonded biomolecular interactions. If this information could be distilled down to nonbonded interaction potentials, these would have some key advantages over standard force fields. However, there are some important outstanding issues to address in order to do this successfully. This paper introduces the protein-ligand informatics "force field", PLIff, which begins to address these key challenges ( https://bitbucket.org/AstexUK/pli ). As a result of their knowledge-based nature, the next-generation nonbonded potentials that make up PLIff automatically capture a wide range of interaction types, including special interactions that are often poorly described by standard force fields. We illustrate how PLIff may be used in structure-based design applications, including interaction fields, fragment mapping, and protein-ligand docking. PLIff performs at least as well as state-of-the art scoring functions in terms of pose predictions and ranking compounds in a virtual screening context.

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

International Nuclear Information System (INIS)

Asplund, M; Thaning, E; Von Holst, H; Lundberg, J; Sandberg-Nordqvist, A C; Kostyszyn, B; Inganaes, O

2009-01-01

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.

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

Science.gov (United States)

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

2010-11-01

Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a C(α)-based coarse-grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP-GPU program). We assessed the computational performance of an end-to-end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ∼90-fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force-extension profiles using experimental pulling speeds (v(f) = 1-10 μm/s) employed in atomic force microscopy and in optical tweezers-based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10-fold increase in v(f). This implies that, to resolve accurately the free energy landscape and to relate the results of single-molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall-clock time for biomolecules of size as large as 10(5) residues using the SOP-GPU package. © 2010 Wiley-Liss, Inc.

A biomolecular recognition approach for the functionalization of cellulose with gold nanoparticles.

Science.gov (United States)

Almeida, A; Rosa, A M M; Azevedo, A M; Prazeres, D M F

2017-09-01

Materials with new and improved functionalities can be obtained by modifying cellulose with gold nanoparticles (AuNPs) via the in situ reduction of a gold precursor or the deposition or covalent immobilization of pre-synthesized AuNPs. Here, we present an alternative biomolecular recognition approach to functionalize cellulose with biotin-AuNPs that relies on a complex of 2 recognition elements: a ZZ-CBM3 fusion that combines a carbohydrate-binding module (CBM) with the ZZ fragment of the staphylococcal protein A and an anti-biotin antibody. Paper and cellulose microparticles with AuNPs immobilized via the ZZ-CBM3:anti-biotin IgG supramolecular complex displayed an intense red color, whereas essentially no color was detected when AuNPs were deposited over the unmodified materials. Scanning electron microscopy analysis revealed a homogeneous distribution of AuNPs when immobilized via ZZ-CBM3:anti-biotin IgG complexes and aggregation of AuNPs when deposited over paper, suggesting that color differences are due to interparticle plasmon coupling effects. The approach could be used to functionalize paper substrates and cellulose nanocrystals with AuNPs. More important, however, is the fact that the occurrence of a biomolecular recognition event between the CBM-immobilized antibody and its specific, AuNP-conjugated antigen is signaled by red color. This opens up the way for the development of simple and straightforward paper/cellulose-based tests where detection of a target analyte can be made by direct use of color signaling. Copyright © 2017 John Wiley & Sons, Ltd.

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

Directory of Open Access Journals (Sweden)

Alexander Gust

2014-09-01

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

Hybrid quantum information processing

Energy Technology Data Exchange (ETDEWEB)

Furusawa, Akira [Department of Applied Physics, School of Engineering, The University of Tokyo (Japan)

2014-12-04

I will briefly explain the definition and advantage of hybrid quantum information processing, which is hybridization of qubit and continuous-variable technologies. The final goal would be realization of universal gate sets both for qubit and continuous-variable quantum information processing with the hybrid technologies. For that purpose, qubit teleportation with a continuousvariable teleporter is one of the most important ingredients.

Optimal number of coarse-grained sites in different components of large biomolecular complexes.

Science.gov (United States)

Sinitskiy, Anton V; Saunders, Marissa G; Voth, Gregory A

2012-07-26

The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.

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…

Single-molecule pull-down (SiMPull) for new-age biochemistry: methodology and biochemical applications of single-molecule pull-down (SiMPull) for probing biomolecular interactions in crude cell extracts.

Science.gov (United States)

Aggarwal, Vasudha; Ha, Taekjip

2014-11-01

Macromolecular interactions play a central role in many biological processes. Protein-protein interactions have mostly been studied by co-immunoprecipitation, which cannot provide quantitative information on all possible molecular connections present in the complex. We will review a new approach that allows cellular proteins and biomolecular complexes to be studied in real-time at the single-molecule level. This technique is called single-molecule pull-down (SiMPull), because it integrates principles of conventional immunoprecipitation with the powerful single-molecule fluorescence microscopy. SiMPull is used to count how many of each protein is present in the physiological complexes found in cytosol and membranes. Concurrently, it serves as a single-molecule biochemical tool to perform functional studies on the pulled-down proteins. In this review, we will focus on the detailed methodology of SiMPull, its salient features and a wide range of biological applications in comparison with other biosensing tools. © 2014 WILEY Periodicals, Inc.

Information in general medical practices: the information processing model.

Science.gov (United States)

Crowe, Sarah; Tully, Mary P; Cantrill, Judith A

2010-04-01

The need for effective communication and handling of secondary care information in general practices is paramount. To explore practice processes on receiving secondary care correspondence in a way that integrates the information needs and perceptions of practice staff both clinical and administrative. Qualitative study using semi-structured interviews with a wide range of practice staff (n = 36) in nine practices in the Northwest of England. Analysis was based on the framework approach using N-Vivo software and involved transcription, familiarization, coding, charting, mapping and interpretation. The 'information processing model' was developed to describe the six stages involved in practice processing of secondary care information. These included the amendment or updating of practice records whilst simultaneously or separately actioning secondary care recommendations, using either a 'one-step' or 'two-step' approach, respectively. Many factors were found to influence each stage and impact on the continuum of patient care. The primary purpose of processing secondary care information is to support patient care; this study raises the profile of information flow and usage within practices as an issue requiring further consideration.

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

CERN Multimedia

CERN. Geneva

2016-01-01

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

Information-processing genes

International Nuclear Information System (INIS)

Tahir Shah, K.

1995-01-01

There are an estimated 100,000 genes in the human genome of which 97% is non-coding. On the other hand, bacteria have little or no non-coding DNA. Non-coding region includes introns, ALU sequences, satellite DNA, and other segments not expressed as proteins. Why it exists? Why nature has kept non-coding during the long evolutionary period if it has no role in the development of complex life forms? Does complexity of a species somehow correlated to the existence of apparently useless sequences? What kind of capability is encoded within such nucleotide sequences that is a necessary, but not a sufficient condition for the evolution of complex life forms, keeping in mind the C-value paradox and the omnipresence of non-coding segments in higher eurkaryotes and also in many archea and prokaryotes. The physico-chemical description of biological processes is hardware oriented and does not highlight algorithmic or information processing aspect. However, an algorithm without its hardware implementation is useless as much as hardware without its capability to run an algorithm. The nature and type of computation an information-processing hardware can perform depends only on its algorithm and the architecture that reflects the algorithm. Given that enormously difficult tasks such as high fidelity replication, transcription, editing and regulation are all achieved within a long linear sequence, it is natural to think that some parts of a genome are involved is these tasks. If some complex algorithms are encoded with these parts, then it is natural to think that non-coding regions contain processing-information algorithms. A comparison between well-known automatic sequences and sequences constructed out of motifs is found in all species proves the point: noncoding regions are a sort of ''hardwired'' programs, i.e., they are linear representations of information-processing machines. Thus in our model, a noncoding region, e.g., an intron contains a program (or equivalently, it is

Infochemistry Information Processing at the Nanoscale

CERN Document Server

Szacilowski, Konrad

2012-01-01

Infochemistry: Information Processing at the Nanoscale, defines a new field of science, and describes the processes, systems and devices at the interface between chemistry and information sciences. The book is devoted to the application of molecular species and nanostructures to advanced information processing. It includes the design and synthesis of suitable materials and nanostructures, their characterization, and finally applications of molecular species and nanostructures for information storage and processing purposes. Divided into twelve chapters; the first three chapters serve as an int

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…

Quantum information processing

National Research Council Canada - National Science Library

Leuchs, Gerd; Beth, Thomas

2003-01-01

... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.5 SimulationofHamiltonians... References... 1 1 1 3 5 8 10 2 Quantum Information Processing and Error Correction with Jump Codes (G. Alber, M. Mussinger...

PREFACE: Quantum information processing

Science.gov (United States)

Briggs, Andrew; Ferry, David; Stoneham, Marshall

2006-05-01

Microelectronics and the classical information technologies transformed the physics of semiconductors. Photonics has given optical materials a new direction. Quantum information technologies, we believe, will have immense impact on condensed matter physics. The novel systems of quantum information processing need to be designed and made. Their behaviours must be manipulated in ways that are intrinsically quantal and generally nanoscale. Both in this special issue and in previous issues (see e.g., Spiller T P and Munro W J 2006 J. Phys.: Condens. Matter 18 V1-10) we see the emergence of new ideas that link the fundamentals of science to the pragmatism of market-led industry. We hope these papers will be followed by many others on quantum information processing in the Journal of Physics: Condensed Matter.

Spin valve sensor for biomolecular identification: Design, fabrication, and characterization

Science.gov (United States)

Li, Guanxiong

Biomolecular identification, e.g., DNA recognition, has broad applications in biology and medicine such as gene expression analysis, disease diagnosis, and DNA fingerprinting. Therefore, we have been developing a magnetic biodetection technology based on giant magnetoresistive spin valve sensors and magnetic nanoparticle (developed for the magnetic nanoparticle detection, assuming the equivalent average field of magnetic nanoparticles and the coherent rotation of spin valve free layer magnetization. Micromagnetic simulations have also been performed for the spin valve sensors. The analytical model and micromagnetic simulations are found consistent with each other and are in good agreement with experiments. The prototype spin valve sensors have been fabricated at both micron and submicron scales. We demonstrated the detection of a single 2.8-mum magnetic microbead by micron-sized spin valve sensors. Based on polymer-mediated self-assembly and fine lithography, a bilayer lift-off process was developed to deposit magnetic nanoparticles onto the sensor surface in a controlled manner. With the lift-off deposition method, we have successfully demonstrated the room temperature detection of monodisperse 16-nm Fe3O 4 nanoparticles in a quantity from a few tens to several hundreds by submicron spin valve sensors, proving the feasibility of the nanoparticle detection. As desired for quantitative biodetection, a fairly linear dependence of sensor signal on the number of nanoparticles has been confirmed. The initial detection of DNA hybridization events labeled by magnetic nanoparticles further proved the magnetic biodetection concept.

Social Information Processing in Deaf Adolescents

Science.gov (United States)

Torres, Jesús; Saldaña, David; Rodríguez-Ortiz, Isabel R.

2016-01-01

The goal of this study was to compare the processing of social information in deaf and hearing adolescents. A task was developed to assess social information processing (SIP) skills of deaf adolescents based on Crick and Dodge's (1994; A review and reformulation of social information-processing mechanisms in children's social adjustment.…

Links between attachment and social information processing: examination of intergenerational processes.

Science.gov (United States)

Dykas, Matthew J; Ehrlich, Katherine B; Cassidy, Jude

2011-01-01

This chapter describes theory and research on intergenerational connections between parents' attachment and children's social information processing, as well as between parents' social information processing and children's attachment. The chapter begins with a discussion of attachment theorists' early insights into the role that social information processing plays in attachment processes. Next, current theory about the mechanisms through which cross-generational links between attachment and social information processing might emerge is presented. The central proposition is that the quality of attachment and/or the social information processing of the parent contributes to the quality of attachment and/or social information processing in the child, and these links emerge through mediating processes related to social learning, open communication, gate-keeping, emotion regulation, and joint attention. A comprehensive review of the literature is then presented. The chapter ends with the presentation of a current theoretical perspective and suggestions for future empirical and clinical endeavors.

Correlated Heterospectral Lipidomics for Biomolecular Profiling of Remyelination in Multiple Sclerosis

Directory of Open Access Journals (Sweden)

Mads S. Bergholt

2017-12-01

Full Text Available Analyzing lipid composition and distribution within the brain is important to study white matter pathologies that present focal demyelination lesions, such as multiple sclerosis. Some lesions can endogenously re-form myelin sheaths. Therapies aim to enhance this repair process in order to reduce neurodegeneration and disability progression in patients. In this context, a lipidomic analysis providing both precise molecular classification and well-defined localization is crucial to detect changes in myelin lipid content. Here we develop a correlated heterospectral lipidomic (HSL approach based on coregistered Raman spectroscopy, desorption electrospray ionization mass spectrometry (DESI-MS, and immunofluorescence imaging. We employ HSL to study the structural and compositional lipid profile of demyelination and remyelination in an induced focal demyelination mouse model and in multiple sclerosis lesions from patients ex vivo. Pixelwise coregistration of Raman spectroscopy and DESI-MS imaging generated a heterospectral map used to interrelate biomolecular structure and composition of myelin. Multivariate regression analysis enabled Raman-based assessment of highly specific lipid subtypes in complex tissue for the first time. This method revealed the temporal dynamics of remyelination and provided the first indication that newly formed myelin has a different lipid composition compared to normal myelin. HSL enables detailed molecular myelin characterization that can substantially improve upon the current understanding of remyelination in multiple sclerosis and provides a strategy to assess remyelination treatments in animal models.

Evaluation of biomolecular distributions in rat brain tissues by means of ToF-SIMS using a continuous beam of Ar clusters.

Science.gov (United States)

Nakano, Shusuke; Yokoyama, Yuta; Aoyagi, Satoka; Himi, Naoyuki; Fletcher, John S; Lockyer, Nicholas P; Henderson, Alex; Vickerman, John C

2016-06-08

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) provides detailed chemical structure information and high spatial resolution images. Therefore, ToF-SIMS is useful for studying biological phenomena such as ischemia. In this study, in order to evaluate cerebral microinfarction, the distribution of biomolecules generated by ischemia was measured with ToF-SIMS. ToF-SIMS data sets were analyzed by means of multivariate analysis for interpreting complex samples containing unknown information and to obtain biomolecular mapping indicated by fragment ions from the target biomolecules. Using conventional ToF-SIMS (primary ion source: Bi cluster ion), it is difficult to detect secondary ions beyond approximately 1000 u. Moreover, the intensity of secondary ions related to biomolecules is not always high enough for imaging because of low concentration even if the masses are lower than 1000 u. However, for the observation of biomolecular distributions in tissues, it is important to detect low amounts of biological molecules from a particular area of tissue. Rat brain tissue samples were measured with ToF-SIMS (J105, Ionoptika, Ltd., Chandlers Ford, UK), using a continuous beam of Ar clusters as a primary ion source. ToF-SIMS with Ar clusters efficiently detects secondary ions related to biomolecules and larger molecules. Molecules detected by ToF-SIMS were examined by analyzing ToF-SIMS data using multivariate analysis. Microspheres (45 μm diameter) were injected into the rat unilateral internal carotid artery (MS rat) to cause cerebral microinfarction. The rat brain was sliced and then measured with ToF-SIMS. The brain samples of a normal rat and the MS rat were examined to find specific secondary ions related to important biomolecules, and then the difference between them was investigated. Finally, specific secondary ions were found around vessels incorporating microspheres in the MS rat. The results suggest that important biomolecules related to cerebral

"Peak tracking chip" for label-free optical detection of bio-molecular interaction and bulk sensing.

Science.gov (United States)

Bougot-Robin, Kristelle; Li, Shunbo; Zhang, Yinghua; Hsing, I-Ming; Benisty, Henri; Wen, Weijia

2012-10-21

A novel imaging method for bulk refractive index sensing or label-free bio-molecular interaction sensing is presented. This method is based on specially designed "Peak tracking chip" (PTC) involving "tracks" of adjacent resonant waveguide gratings (RWG) "micropads" with slowly evolving resonance position. Using a simple camera the spatial information robustly retrieves the diffraction efficiency, which in turn transduces either the refractive index of the liquids on the tracks or the effective thickness of an immobilized biological layer. Our intrinsically multiplex chip combines tunability and versatility advantages of dielectric guided wave biochips without the need of costly hyperspectral instrumentation. The current success of surface plasmon imaging techniques suggests that our chip proposal could leverage an untapped potential to routinely extend such techniques in a convenient and sturdy optical configuration toward, for instance for large analytes detection. PTC design and fabrication are discussed with challenging process to control micropads properties by varying their period (step of 2 nm) or their duty cycle through the groove width (steps of 4 nm). Through monochromatic imaging of our PTC, we present experimental demonstration of bulk index sensing on the range [1.33-1.47] and of surface biomolecule detection of molecular weight 30 kDa in aqueous solution using different surface densities. A sensitivity of the order of 10(-5) RIU for bulk detection and a sensitivity of the order of ∼10 pg mm(-2) for label-free surface detection are expected, therefore opening a large range of application of our chip based imaging technique. Exploiting and chip design, we expect as well our chip to open new direction for multispectral studies through imaging.

Dose controlled low energy electron irradiator for biomolecular films.

Science.gov (United States)

Kumar, S V K; Tare, Satej T; Upalekar, Yogesh V; Tsering, Thupten

2016-03-01

We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at -20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

A fast mollified impulse method for biomolecular atomistic simulations

Energy Technology Data Exchange (ETDEWEB)

Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)

2017-03-15

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

Dose controlled low energy electron irradiator for biomolecular films

Energy Technology Data Exchange (ETDEWEB)

Kumar, S. V. K., E-mail: svkk@tifr.res.in; Tare, Satej T.; Upalekar, Yogesh V.; Tsering, Thupten [Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

2016-03-15

We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at −20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

Process information systems in nuclear reprocessing

International Nuclear Information System (INIS)

Jaeschke, A.; Keller, H.; Orth, H.

1987-01-01

On a production management level, a process information system in a nuclear reprocessing plant (NRP) has to fulfill conventional operating functions and functions for nuclear material surveillance (safeguards). Based on today's state of the art of on-line process control technology, the progress in hardware and software technology allows to introduce more process-specific intelligence into process information systems. Exemplified by an expert-system-aided laboratory management system as component of a NRP process information system, the paper demonstrates that these technologies can be applied already. (DG) [de

Process-aware information systems : lessons to be learned from process mining

NARCIS (Netherlands)

Aalst, van der W.M.P.; Jensen, K.; Aalst, van der W.M.P.

2009-01-01

A Process-Aware Information System (PAIS) is a software system that manages and executes operational processes involving people, applications, and/or information sources on the basis of process models. Example PAISs are workflow management systems, case-handling systems, enterprise information

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),enzyme-linkedimmunosorbentassay(EIA...... 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...

SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces.

Science.gov (United States)

Kochanczyk, Marek; Hlavacek, William S; Lipniacki, Tomasz

2017-11-15

Rule-based modeling is a powerful approach for studying biomolecular site dynamics. Here, we present SPATKIN, a general-purpose simulator for rule-based modeling in two spatial dimensions. The simulation algorithm is a lattice-based method that tracks Brownian motion of individual molecules and the stochastic firing of rule-defined reaction events. Because rules are used as event generators, the algorithm is network-free, meaning that it does not require to generate the complete reaction network implied by rules prior to simulation. In a simulation, each molecule (or complex of molecules) is taken to occupy a single lattice site that cannot be shared with another molecule (or complex). SPATKIN is capable of simulating a wide array of membrane-associated processes, including adsorption, desorption and crowding. Models are specified using an extension of the BioNetGen language, which allows to account for spatial features of the simulated process. The C ++ source code for SPATKIN is distributed freely under the terms of the GNU GPLv3 license. The source code can be compiled for execution on popular platforms (Windows, Mac and Linux). An installer for 64-bit Windows and a macOS app are available. The source code and precompiled binaries are available at the SPATKIN Web site (http://pmbm.ippt.pan.pl/software/spatkin). spatkin.simulator@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Information-Processing Models and Curriculum Design

Science.gov (United States)

Calfee, Robert C.

1970-01-01

"This paper consists of three sections--(a) the relation of theoretical analyses of learning to curriculum design, (b) the role of information-processing models in analyses of learning processes, and (c) selected examples of the application of information-processing models to curriculum design problems." (Author)

BRICS and Quantum Information Processing

DEFF Research Database (Denmark)

Schmidt, Erik Meineche

1998-01-01

BRICS is a research centre and international PhD school in theoretical computer science, based at the University of Aarhus, Denmark. The centre has recently become engaged in quantum information processing in cooperation with the Department of Physics, also University of Aarhus. This extended...... abstract surveys activities at BRICS with special emphasis on the activities in quantum information processing....

Risk perception and information processing: the development and validation of a questionnaire to assess self-reported information processing.

Science.gov (United States)

Smerecnik, Chris M R; Mesters, Ilse; Candel, Math J J M; De Vries, Hein; De Vries, Nanne K

2012-01-01

The role of information processing in understanding people's responses to risk information has recently received substantial attention. One limitation of this research concerns the unavailability of a validated questionnaire of information processing. This article presents two studies in which we describe the development and validation of the Information-Processing Questionnaire to meet that need. Study 1 describes the development and initial validation of the questionnaire. Participants were randomized to either a systematic processing or a heuristic processing condition after which they completed a manipulation check and the initial 15-item questionnaire and again two weeks later. The questionnaire was subjected to factor reliability and validity analyses on both measurement times for purposes of cross-validation of the results. A two-factor solution was observed representing a systematic processing and a heuristic processing subscale. The resulting scale showed good reliability and validity, with the systematic condition scoring significantly higher on the systematic subscale and the heuristic processing condition significantly higher on the heuristic subscale. Study 2 sought to further validate the questionnaire in a field study. Results of the second study corresponded with those of Study 1 and provided further evidence of the validity of the Information-Processing Questionnaire. The availability of this information-processing scale will be a valuable asset for future research and may provide researchers with new research opportunities. © 2011 Society for Risk Analysis.

Information processing among high-performance managers

Directory of Open Access Journals (Sweden)

S.C. Garcia-Santos

2010-01-01

Full Text Available The purpose of this study was to evaluate the information processing of 43 business managers with a professional superior performance. The theoretical framework considers three models: the Theory of Managerial Roles of Henry Mintzberg, the Theory of Information Processing, and Process Model Response to Rorschach by John Exner. The participants have been evaluated by Rorschach method. The results show that these managers are able to collect data, evaluate them and establish rankings properly. At same time, they are capable of being objective and accurate in the problems assessment. This information processing style permits an interpretation of the world around on basis of a very personal and characteristic processing way or cognitive style.

The laboratory technology of discrete molecular separation: the historical development of gel electrophoresis and the material epistemology of biomolecular science, 1945-1970.

Science.gov (United States)

Chiang, Howard Hsueh-hao

2009-01-01

Preparative and analytical methods developed by separation scientists have played an important role in the history of molecular biology. One such early method is gel electrophoresis, a technique that uses various types of gel as its supporting medium to separate charged molecules based on size and other properties. Historians of science, however, have only recently begun to pay closer attention to this material epistemological dimension of biomolecular science. This paper substantiates the historiographical thread that explores the relationship between modern laboratory practice and the production of scientific knowledge. It traces the historical development of gel electrophoresis from the mid-1940s to the mid-1960s, with careful attention to the interplay between technical developments and disciplinary shifts, especially the rise of molecular biology in this time-frame. Claiming that the early 1950s marked a decisive shift in the evolution of electrophoretic methods from moving boundary to zone electrophoresis, I reconstruct various trajectories in which scientists such as Oliver Smithies sought out the most desirable solid supporting medium for electrophoretic instrumentation. Biomolecular knowledge, I argue, emerged in part from this process of seeking the most appropriate supporting medium that allowed for discrete molecular separation and visualization. The early 1950s, therefore, marked not only an important turning point in the history of separation science, but also a transformative moment in the history of the life sciences as the growth of molecular biology depended in part on the epistemological access to the molecular realm available through these evolving technologies.

Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

Science.gov (United States)

Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

2018-02-05

Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

Proprioceptive information processing in schizophrenia

DEFF Research Database (Denmark)

Arnfred, Sidse M H

of the left somatosensory cortex and it was suggested to be in accordance with two theories of schizophrenic information processing: the theory of deficiency of corollary discharge and the theory of weakening of the influence of past regularities. No gating deficiency was observed and the imprecision...... Rado (1890-1972) suggested that one of two un-reducible deficits in schizophrenia was a disorder of proprioception. Exploration of proprioceptive information processing is possible through the measurement of evoked and event related potentials. Event related EEG can be analyzed as conventional time...... and amplitude attenuation was not a general phenomenon across the entire brain response. Summing up, in support of Rado's hypothesis, schizophrenia spectrum patients demonstrated abnormalities in proprioceptive information processing. Future work needs to extend the findings in larger un-medicated, non...

Hierarchical process memory: memory as an integral component of information processing

Science.gov (United States)

Hasson, Uri; Chen, Janice; Honey, Christopher J.

2015-01-01

Models of working memory commonly focus on how information is encoded into and retrieved from storage at specific moments. However, in the majority of real-life processes, past information is used continuously to process incoming information across multiple timescales. Considering single unit, electrocorticography, and functional imaging data, we argue that (i) virtually all cortical circuits can accumulate information over time, and (ii) the timescales of accumulation vary hierarchically, from early sensory areas with short processing timescales (tens to hundreds of milliseconds) to higher-order areas with long processing timescales (many seconds to minutes). In this hierarchical systems perspective, memory is not restricted to a few localized stores, but is intrinsic to information processing that unfolds throughout the brain on multiple timescales. “The present contains nothing more than the past, and what is found in the effect was already in the cause.”Henri L Bergson PMID:25980649

An information theory-based approach to modeling the information processing of NPP operators

International Nuclear Information System (INIS)

Kim, Jong Hyun; Seong, Poong Hyun

2002-01-01

This paper proposes a quantitative approach to modeling the information processing of NPP operators. The aim of this work is to derive the amount of the information processed during a certain control task. The focus will be on i) developing a model for information processing of NPP operators and ii) quantifying the model. To resolve the problems of the previous approaches based on the information theory, i.e. the problems of single channel approaches, we primarily develop the information processing model having multiple stages, which contains information flows. Then the uncertainty of the information is quantified using the Conant's model, a kind of information theory

40 CFR 68.65 - Process safety information.

Science.gov (United States)

2010-07-01

... (CONTINUED) CHEMICAL ACCIDENT PREVENTION PROVISIONS Program 3 Prevention Program § 68.65 Process safety... 40 Protection of Environment 15 2010-07-01 2010-07-01 false Process safety information. 68.65... compilation of written process safety information before conducting any process hazard analysis required by...

Information management in process planning

NARCIS (Netherlands)

Lutters, Diederick; Wijnker, T.C.; Kals, H.J.J.

1999-01-01

A recently proposed reference model indicates the use of structured information as the basis for the control of design and manufacturing processes. The model is used as a basis to describe the integration of design and process planning. A differentiation is made between macro- and micro process

Aligning Business Process Quality and Information System Quality

OpenAIRE

Heinrich, Robert

2013-01-01

Business processes and information systems mutually affect each other in non-trivial ways. Frequently, the business process design and the information system design are not well aligned. This means that business processes are designed without taking the information system impact into account, and vice versa. Missing alignment at design time often results in quality problems at runtime, such as large response times of information systems, large process execution times, overloaded information s...

Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics

Science.gov (United States)

Sinitskiy, Anton V.; Pande, Vijay S.

2018-01-01

Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD) trajectory from the set of trajectories used to build the MSM. A rule of thumb claiming that the slowest implicit time scale captured by an MSM should be comparable by the order of magnitude to the aggregate duration of all MD trajectories used to build this MSM has been known in the field. However, this rule has never been formally proved. In this work, we present analytical results for the slowest time scale in several types of MSMs, supporting the above rule. We conclude that the slowest implicit time scale equals the product of the aggregate sampling and four factors that quantify: (1) how much statistics on the conformational transitions corresponding to the longest implicit time scale is available, (2) how good the sampling of the destination Markov state is, (3) the gain in statistics from using a sliding window for counting transitions between Markov states, and (4) a bias in the estimate of the implicit time scale arising from finite sampling of the conformational transitions. We demonstrate that in many practically important cases all these four factors are on the order of unity, and we analyze possible scenarios that could lead to their significant deviation from unity. Overall, we provide for the first time analytical results on the slowest time scales captured by MSMs. These results can guide further practical applications of MSMs to biomolecular dynamics and allow for higher computational efficiency of simulations.

Science-based information processing in the process control of power stations

International Nuclear Information System (INIS)

Weisang, C.

1992-01-01

Through the application of specialized systems, future-orientated information processing integrates the sciences of processes, control systems, process control strategies, user behaviour and ergonomics. Improvements in process control can be attained, inter alia, by the preparation of the information contained (e.g. by suppressing the flow of signals and replacing it with signals which are found on substance) and also by an ergonomic representation of the study of the process. (orig.) [de

Moral Judgment as Information Processing: An Integrative Review

Directory of Open Access Journals (Sweden)

Steve eGuglielmo

2015-10-01

Full Text Available This article reviews dominant models of moral judgment, organizing them within an overarching framework of information processing. This framework poses two fundamental questions: (1 What input information guides moral judgments?; and (2 What psychological processes generate these judgments? Information Models address the first question, identifying critical information elements (including causality, intentionality, and mental states that shape moral judgments. A subclass of Biased Information Models holds that perceptions of these information elements are themselves driven by prior moral judgments. Processing Models address the second question, and existing models have focused on the relative contribution of intuitive versus deliberative processes. This review organizes existing moral judgment models within this framework, critically evaluates them on empirical and theoretical grounds, outlines a general integrative model grounded in information processing, and offers conceptual and methodological suggestions for future research. The information processing perspective provides a useful theoretical framework for organizing extant and future work in the rapidly growing field of moral judgment.

Moral judgment as information processing: an integrative review.

Science.gov (United States)

Guglielmo, Steve

2015-01-01

How do humans make moral judgments about others' behavior? This article reviews dominant models of moral judgment, organizing them within an overarching framework of information processing. This framework poses two distinct questions: (1) What input information guides moral judgments? and (2) What psychological processes generate these judgments? Information Models address the first question, identifying critical information elements (including causality, intentionality, and mental states) that shape moral judgments. A subclass of Biased Information Models holds that perceptions of these information elements are themselves driven by prior moral judgments. Processing Models address the second question, and existing models have focused on the relative contribution of intuitive versus deliberative processes. This review organizes existing moral judgment models within this framework and critically evaluates them on empirical and theoretical grounds; it then outlines a general integrative model grounded in information processing, and concludes with conceptual and methodological suggestions for future research. The information-processing framework provides a useful theoretical lens through which to organize extant and future work in the rapidly growing field of moral judgment.

Moral judgment as information processing: an integrative review

Science.gov (United States)

Guglielmo, Steve

2015-01-01

How do humans make moral judgments about others’ behavior? This article reviews dominant models of moral judgment, organizing them within an overarching framework of information processing. This framework poses two distinct questions: (1) What input information guides moral judgments? and (2) What psychological processes generate these judgments? Information Models address the first question, identifying critical information elements (including causality, intentionality, and mental states) that shape moral judgments. A subclass of Biased Information Models holds that perceptions of these information elements are themselves driven by prior moral judgments. Processing Models address the second question, and existing models have focused on the relative contribution of intuitive versus deliberative processes. This review organizes existing moral judgment models within this framework and critically evaluates them on empirical and theoretical grounds; it then outlines a general integrative model grounded in information processing, and concludes with conceptual and methodological suggestions for future research. The information-processing framework provides a useful theoretical lens through which to organize extant and future work in the rapidly growing field of moral judgment. PMID:26579022

Process-aware information systems : design, enactment and analysis

NARCIS (Netherlands)

Aalst, van der W.M.P.; Wah, B.W.

2009-01-01

Process-aware information systems support operational business processes by combining advances in information technology with recent insights from management science. Workflow management systems are typical examples of such systems. However, many other types of information systems are also "process

Information Limited Oligonucleotide Amplification Assay for Affinity-Based, Parallel Detection Studies.

Directory of Open Access Journals (Sweden)

Harish Bokkasam

Full Text Available Molecular communication systems encounter similar constraints as telecommunications. In either case, channel crosstalk at the receiver end will result in information loss that statistical analysis cannot compensate. This is because in any communication channel there is a physical limit to the amount of information that can be transmitted. We present a novel and simple modified end amplification (MEA technique to generate reduced and defined amounts of specific information in form of short fragments from an oligonucleotide source that also contains unrelated and redundant information. Our method can be a valuable tool to investigate information overflow and channel capacity in biomolecular recognition systems.

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

Science.gov (United States)

Alford, Rebecca F; Leaver-Fay, Andrew; Gonzales, Lynda; Dolan, Erin L; Gray, Jeffrey J

2017-12-01

Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community. This 10-week summer program begins with one week of training on computational biology methods development, transitions to eight weeks of research, and culminates in one week at the Rosetta annual conference. To date, two cohorts of students have participated, tackling research topics including vaccine design, enzyme design, protein-based materials, glycoprotein modeling, crowd-sourced science, RNA processing, hydrogen bond networks, and amyloid formation. Students in the program report outcomes comparable to students who participate in similar in-person programs. These outcomes include the development of a sense of community and increases in their scientific self-efficacy, scientific identity, and science values, all predictors of continuing in a science research career. Furthermore, the program attracted students from diverse backgrounds, which demonstrates the potential of this approach to broaden the participation of young scientists from backgrounds traditionally underrepresented in computational biology.

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

Directory of Open Access Journals (Sweden)

Rebecca F Alford

2017-12-01

Full Text Available Computational biology is an interdisciplinary field, and many computational biology research projects involve distributed teams of scientists. To accomplish their work, these teams must overcome both disciplinary and geographic barriers. Introducing new training paradigms is one way to facilitate research progress in computational biology. Here, we describe a new undergraduate program in biomolecular structure prediction and design in which students conduct research at labs located at geographically-distributed institutions while remaining connected through an online community. This 10-week summer program begins with one week of training on computational biology methods development, transitions to eight weeks of research, and culminates in one week at the Rosetta annual conference. To date, two cohorts of students have participated, tackling research topics including vaccine design, enzyme design, protein-based materials, glycoprotein modeling, crowd-sourced science, RNA processing, hydrogen bond networks, and amyloid formation. Students in the program report outcomes comparable to students who participate in similar in-person programs. These outcomes include the development of a sense of community and increases in their scientific self-efficacy, scientific identity, and science values, all predictors of continuing in a science research career. Furthermore, the program attracted students from diverse backgrounds, which demonstrates the potential of this approach to broaden the participation of young scientists from backgrounds traditionally underrepresented in computational biology.

Bookshelf: a simple curation system for the storage of biomolecular simulation data.

Science.gov (United States)

Vohra, Shabana; Hall, Benjamin A; Holdbrook, Daniel A; Khalid, Syma; Biggin, Philip C

2010-01-01

Molecular dynamics simulations can now routinely generate data sets of several hundreds of gigabytes in size. The ability to generate this data has become easier over recent years and the rate of data production is likely to increase rapidly in the near future. One major problem associated with this vast amount of data is how to store it in a way that it can be easily retrieved at a later date. The obvious answer to this problem is a database. However, a key issue in the development and maintenance of such a database is its sustainability, which in turn depends on the ease of the deposition and retrieval process. Encouraging users to care about meta-data is difficult and thus the success of any storage system will ultimately depend on how well used by end-users the system is. In this respect we suggest that even a minimal amount of metadata if stored in a sensible fashion is useful, if only at the level of individual research groups. We discuss here, a simple database system which we call 'Bookshelf', that uses python in conjunction with a mysql database to provide an extremely simple system for curating and keeping track of molecular simulation data. It provides a user-friendly, scriptable solution to the common problem amongst biomolecular simulation laboratories; the storage, logging and subsequent retrieval of large numbers of simulations. Download URL: http://sbcb.bioch.ox.ac.uk/bookshelf/

Information paths within the new product development process

DEFF Research Database (Denmark)

Jespersen, Kristina Risom

2007-01-01

collection platform to obtain measurements from within the NPD process. 42 large, international companies participated in the data collecting simulation. Results revealed five different information paths that were not connecting all stages of the NPD process. Moreover, results show that the front......-end is not driving the information acquisition through the stages of the NPD process, and that environmental turbulence disconnects stages from the information paths in the NPD process. This implies that information is at the same time a key to success and a key to entrapment in the NPD process....

Process-aware information systems : bridging people and software through process technology

NARCIS (Netherlands)

Dumas, M.; Aalst, van der W.M.P.; Hofstede, ter A.H.M.

2005-01-01

A unifying foundation to design and implement process-aware information systems This publication takes on the formidable task of establishing a unifying foundation and set of common underlying principles to effectively model, design, and implement process-aware information systems. Authored by

Advances in microbial leaching processes for nickel extraction from lateritic minerals - A review

International Nuclear Information System (INIS)

Behra, Sunil Kumar; Mulaba-Bafubiandi, Antoine Floribert

2015-01-01

Lateritic nickel minerals constitute about 80% of nickel reserves in the world, but their contribution for nickel production is about 40%. The obstacles in extraction of nickel from lateritic minerals are attributed to their very complex mineralogy and low nickel content. Hence, the existing metallurgical techniques are not techno-economically feasible and environmentally sustainable for processing of such complex deposits. At this juncture, microbial mineral processing could be a benevolent approach for processing of lateritic minerals in favor of nickel extraction. The microbial mineral processing route offers many advantages over conventional metallurgical methods as the process is operated under ambient conditions and requires low energy input; thus these processes are relatively simple and environment friendly. Microbial processing of the lateritic deposits still needs improvement to make it industrially viable. Microorganisms play the pivotal role in mineral bio-processing as they catalyze the extraction of metals from minerals. So it is inevitable to explore the physiological and bio-molecular mechanisms involved in this microbe-mineral interaction. The present article offers comprehensive information about the advances in microbial processes for extraction of nickel from laterites.

Advances in microbial leaching processes for nickel extraction from lateritic minerals - A review

Energy Technology Data Exchange (ETDEWEB)

Behra, Sunil Kumar; Mulaba-Bafubiandi, Antoine Floribert [Faculty of Engineering and the Built Environment, University of Johannesburg, (South Africa)

2015-08-15

Lateritic nickel minerals constitute about 80% of nickel reserves in the world, but their contribution for nickel production is about 40%. The obstacles in extraction of nickel from lateritic minerals are attributed to their very complex mineralogy and low nickel content. Hence, the existing metallurgical techniques are not techno-economically feasible and environmentally sustainable for processing of such complex deposits. At this juncture, microbial mineral processing could be a benevolent approach for processing of lateritic minerals in favor of nickel extraction. The microbial mineral processing route offers many advantages over conventional metallurgical methods as the process is operated under ambient conditions and requires low energy input; thus these processes are relatively simple and environment friendly. Microbial processing of the lateritic deposits still needs improvement to make it industrially viable. Microorganisms play the pivotal role in mineral bio-processing as they catalyze the extraction of metals from minerals. So it is inevitable to explore the physiological and bio-molecular mechanisms involved in this microbe-mineral interaction. The present article offers comprehensive information about the advances in microbial processes for extraction of nickel from laterites.

Scaling the Information Processing Demands of Occupations

Science.gov (United States)

Haase, Richard F.; Jome, LaRae M.; Ferreira, Joaquim Armando; Santos, Eduardo J. R.; Connacher, Christopher C.; Sendrowitz, Kerrin

2011-01-01

The purpose of this study was to provide additional validity evidence for a model of person-environment fit based on polychronicity, stimulus load, and information processing capacities. In this line of research the confluence of polychronicity and information processing (e.g., the ability of individuals to process stimuli from the environment…

Physics as Information Processing

International Nuclear Information System (INIS)

D'Ariano, Giacomo Mauro

2011-01-01

I review some recent advances in foundational research at Pavia QUIT group. The general idea is that there is only Quantum Theory without quantization rules, and the whole Physics - including space-time and relativity - is emergent from the quantum-information processing. And since Quantum Theory itself is axiomatized solely on informational principles, the whole Physics must be reformulated in information-theoretical terms: this is the It from bit of J. A. Wheeler.The review is divided into four parts: a) the informational axiomatization of Quantum Theory; b) how space-time and relativistic covariance emerge from quantum computation; c) what is the information-theoretical meaning of inertial mass and of (ℎ/2π), and how the quantum field emerges; d) an observational consequence of the new quantum field theory: a mass-dependent refraction index of vacuum. I will conclude with the research lines that will follow in the immediate future.

A language for information commerce processes

NARCIS (Netherlands)

Aberer, Karl; Wombacher, Andreas

Automatizing information commerce requires languages to represent the typical information commerce processes. Existing languages and standards cover either only very specific types of business models or are too general to capture in a concise way the specific properties of information commerce

Content Is King: Databases Preserve the Collective Information of Science.

Science.gov (United States)

Yates, John R

2018-04-01

Databases store sequence information experimentally gathered to create resources that further science. In the last 20 years databases have become critical components of fields like proteomics where they provide the basis for large-scale and high-throughput proteomic informatics. Amos Bairoch, winner of the Association of Biomolecular Resource Facilities Frederick Sanger Award, has created some of the important databases proteomic research depends upon for accurate interpretation of data.

A process framework for information security management

Directory of Open Access Journals (Sweden)

Knut Haufe

2016-01-01

Full Text Available Securing sensitive organizational data has become increasingly vital to organizations. An Information Security Management System (ISMS is a systematic approach for establishing, implementing, operating, monitoring, reviewing, maintaining and improving an organization's information security. Key elements of the operation of an ISMS are ISMS processes. However, and in spite of its importance, an ISMS process framework with a description of ISMS processes and their interaction as well as the interaction with other management processes is not available in the literature. Cost benefit analysis of information security investments regarding single measures protecting information and ISMS processes are not in the focus of current research, mostly focused on economics. This article aims to fill this research gap by proposing such an ISMS process framework as the main contribution. Based on a set of agreed upon ISMS processes in existing standards like ISO 27000 series, COBIT and ITIL. Within the framework, identified processes are described and their interaction and interfaces are specified. This framework helps to focus on the operation of the ISMS, instead of focusing on measures and controls. By this, as a main finding, the systemic character of the ISMS consisting of processes and the perception of relevant roles of the ISMS is strengthened.

Cerebro-cerebellar interactions underlying temporal information processing.

Science.gov (United States)

Aso, Kenji; Hanakawa, Takashi; Aso, Toshihiko; Fukuyama, Hidenao

2010-12-01

The neural basis of temporal information processing remains unclear, but it is proposed that the cerebellum plays an important role through its internal clock or feed-forward computation functions. In this study, fMRI was used to investigate the brain networks engaged in perceptual and motor aspects of subsecond temporal processing without accompanying coprocessing of spatial information. Direct comparison between perceptual and motor aspects of time processing was made with a categorical-design analysis. The right lateral cerebellum (lobule VI) was active during a time discrimination task, whereas the left cerebellar lobule VI was activated during a timed movement generation task. These findings were consistent with the idea that the cerebellum contributed to subsecond time processing in both perceptual and motor aspects. The feed-forward computational theory of the cerebellum predicted increased cerebro-cerebellar interactions during time information processing. In fact, a psychophysiological interaction analysis identified the supplementary motor and dorsal premotor areas, which had a significant functional connectivity with the right cerebellar region during a time discrimination task and with the left lateral cerebellum during a timed movement generation task. The involvement of cerebro-cerebellar interactions may provide supportive evidence that temporal information processing relies on the simulation of timing information through feed-forward computation in the cerebellum.

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

International Nuclear Information System (INIS)

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.

PHYSICAL RESOURCES OF INFORMATION PROCESSES AND TECHNOLOGIES

Directory of Open Access Journals (Sweden)

Mikhail O. Kolbanev

2014-11-01

Full Text Available Subject of study. The paper describes basic information technologies for automating of information processes of data storage, distribution and processing in terms of required physical resources. It is shown that the study of these processes with such traditional objectives of modern computer science, as the ability to transfer knowledge, degree of automation, information security, coding, reliability, and others, is not enough. The reasons are: on the one hand, the increase in the volume and intensity of information exchange in the subject of human activity and, on the other hand, drawing near to the limit of information systems efficiency based on semiconductor technologies. Creation of such technologies, which not only provide support for information interaction, but also consume a rational amount of physical resources, has become an actual problem of modern engineering development. Thus, basic information technologies for storage, distribution and processing of information to support the interaction between people are the object of study, and physical temporal, spatial and energy resources required for implementation of these technologies are the subject of study. Approaches. An attempt is made to enlarge the possibilities of traditional cybernetics methodology, which replaces the consideration of material information component by states search for information objects. It is done by taking explicitly into account the amount of physical resources required for changes in the states of information media. Purpose of study. The paper deals with working out of a common approach to the comparison and subsequent selection of basic information technologies for storage, distribution and processing of data, taking into account not only the requirements for the quality of information exchange in particular subject area and the degree of technology application, but also the amounts of consumed physical resources. Main findings. Classification of resources

Piezoelectric tuning fork biosensors for the quantitative measurement of biomolecular interactions

International Nuclear Information System (INIS)

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

2015-01-01

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. (paper)

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

Science.gov (United States)

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

2015-04-14

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

Conjoint Management of Business Processes and Information Technologies

DEFF Research Database (Denmark)

Siurdyban, Artur

and improve business processes. As a consequence, there is a growing need to address managerial aspects of the relationships between information technologies and business processes. The aim of this PhD study is to investigate how the practice of conjoint management of business processes and information...... technologies can be supported and improved. The study is organized into five research papers and this summary. Each paper addresses a different aspect of conjoint management of business processes and information technologies, i.e. problem development and managerial practices on software...... and information technologies in a project environment. It states that both elements are intrinsically related and should be designed and considered together. The second case examines the relationships between information technology management and business process management. It discusses the multi-faceted role...

Synergistic Information Processing Encrypts Strategic Reasoning in Poker.

Science.gov (United States)

Frey, Seth; Albino, Dominic K; Williams, Paul L

2018-06-14

There is a tendency in decision-making research to treat uncertainty only as a problem to be overcome. But it is also a feature that can be leveraged, particularly in social interaction. Comparing the behavior of profitable and unprofitable poker players, we reveal a strategic use of information processing that keeps decision makers unpredictable. To win at poker, a player must exploit public signals from others. But using public inputs makes it easier for an observer to reconstruct that player's strategy and predict his or her behavior. How should players trade off between exploiting profitable opportunities and remaining unexploitable themselves? Using a recent multivariate approach to information theoretic data analysis and 1.75 million hands of online two-player No-Limit Texas Hold'em, we find that the important difference between winning and losing players is not in the amount of information they process, but how they process it. In particular, winning players are better at integrative information processing-creating new information from the interaction between their cards and their opponents' signals. We argue that integrative information processing does not just produce better decisions, it makes decision-making harder for others to reverse engineer, as an expert poker player's cards act like the private key in public-key cryptography. Poker players encrypt their reasoning with the way they process information. The encryption function of integrative information processing makes it possible for players to exploit others while remaining unexploitable. By recognizing the act of information processing as a strategic behavior in its own right, we offer a detailed account of how experts use endemic uncertainty to conceal their intentions in high-stakes competitive environments, and we highlight new opportunities between cognitive science, information theory, and game theory. Copyright © 2018 Cognitive Science Society, Inc.

What do information reuse and automated processing require in engineering design? Semantic process

Directory of Open Access Journals (Sweden)

Ossi Nykänen

2011-12-01

Full Text Available Purpose: The purpose of this study is to characterize, analyze, and demonstrate machine-understandable semantic process for validating, integrating, and processing technical design information. This establishes both a vision and tools for information reuse and semi-automatic processing in engineering design projects, including virtual machine laboratory applications with generated components.Design/methodology/approach: The process model has been developed iteratively in terms of action research, constrained by the existing technical design practices and assumptions (design documents, expert feedback, available technologies (pre-studies and experiments with scripting and pipeline tools, benchmarking with other process models and methods (notably the RUP and DITA, and formal requirements (computability and the critical information paths for the generated applications. In practice, the work includes both quantitative and qualitative components.Findings: Technical design processes may be greatly enhanced in terms of semantic process thinking, by enriching design information, and automating information validation and transformation tasks. Contemporary design information, however, is mainly intended for human consumption, and needs to be explicitly enriched with the currently missing data and interfaces. In practice, this may require acknowledging the role of technical information or knowledge engineer, to lead the development of the semantic design information process in a design organization. There is also a trade-off between machine-readability and system complexity that needs to be studied further, both empirically and in theory.Research limitations/implications: The conceptualization of the semantic process is essentially an abstraction based on the idea of progressive design. While this effectively allows implementing semantic processes with, e.g., pipeline technologies, the abstraction is valid only when technical design is organized into

Animal models for information processing during sleep

NARCIS (Netherlands)

Coenen, A.M.L.; Drinkenburg, W.H.I.M.

2002-01-01

Information provided by external stimuli does reach the brain during sleep, although the amount of information is reduced during sleep compared to wakefulness. The process controlling this reduction is called `sensory' gating and evidence exists that the underlying neurophysiological processes take

Microfluidic Devices for Studying Biomolecular Interactions

Science.gov (United States)

Wilson, Wilbur W.; Garcia, Carlos d.; Henry, Charles S.

2006-01-01

Microfluidic devices for monitoring biomolecular interactions have been invented. These devices are basically highly miniaturized liquid-chromatography columns. They are intended to be prototypes of miniature analytical devices of the laboratory on a chip type that could be fabricated rapidly and inexpensively and that, because of their small sizes, would yield analytical results from very small amounts of expensive analytes (typically, proteins). Other advantages to be gained by this scaling down of liquid-chromatography columns may include increases in resolution and speed, decreases in the consumption of reagents, and the possibility of performing multiple simultaneous and highly integrated analyses by use of multiple devices of this type, each possibly containing multiple parallel analytical microchannels. The principle of operation is the same as that of a macroscopic liquid-chromatography column: The column is a channel packed with particles, upon which are immobilized molecules of the protein of interest (or one of the proteins of interest if there are more than one). Starting at a known time, a solution or suspension containing molecules of the protein or other substance of interest is pumped into the channel at its inlet. The liquid emerging from the outlet of the channel is monitored to detect the molecules of the dissolved or suspended substance(s). The time that it takes these molecules to flow from the inlet to the outlet is a measure of the degree of interaction between the immobilized and the dissolved or suspended molecules. Depending on the precise natures of the molecules, this measure can be used for diverse purposes: examples include screening for solution conditions that favor crystallization of proteins, screening for interactions between drugs and proteins, and determining the functions of biomolecules.

Quantum information processing beyond ten ion-qubits

International Nuclear Information System (INIS)

Monz, T.

2011-01-01

Successful processing of quantum information is, to a large degree, based on two aspects: a) the implementation of high-fidelity quantum gates, as well as b) avoiding or suppressing decoherence processes that destroy quantum information. The presented work shows our progress in the field of experimental quantum information processing over the last years: the implementation and characterisation of several quantum operations, amongst others the first realisation of the quantum Toffoli gate in an ion-trap based quantum computer. The creation of entangled states with up to 14 qubits serves as basis for investigations of decoherence processes. Based on the realised quantum operations as well as the knowledge about dominant noise processes in the employed apparatus, entanglement swapping as well as quantum operations within a decoherence-free subspace are demonstrated. (author) [de

Frequency-scanning MALDI linear ion trap mass spectrometer for large biomolecular ion detection.

Science.gov (United States)

Lu, I-Chung; Lin, Jung Lee; Lai, Szu-Hsueh; Chen, Chung-Hsuan

2011-11-01

This study presents the first report on the development of a matrix-assisted laser desorption ionization (MALDI) linear ion trap mass spectrometer for large biomolecular ion detection by frequency scan. We designed, installed, and tested this radio frequency (RF) scan linear ion trap mass spectrometer and its associated electronics to dramatically extend the mass region to be detected. The RF circuit can be adjusted from 300 to 10 kHz with a set of operation amplifiers. To trap the ions produced by MALDI, a high pressure of helium buffer gas was employed to quench extra kinetic energy of the heavy ions produced by MALDI. The successful detection of the singly charged secretory immunoglobulin A ions indicates that the detectable mass-to-charge ratio (m/z) of this system can reach ~385 000 or beyond.

Introduction to information processing

CERN Document Server

Dietel, Harvey M

2014-01-01

An Introduction to Information Processing provides an informal introduction to the computer field. This book introduces computer hardware, which is the actual computing equipment.Organized into three parts encompassing 12 chapters, this book begins with an overview of the evolution of personal computing and includes detailed case studies on two of the most essential personal computers for the 1980s, namely, the IBM Personal Computer and Apple's Macintosh. This text then traces the evolution of modern computing systems from the earliest mechanical calculating devices to microchips. Other chapte

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

A quantitative approach to modeling the information processing of NPP operators under input information overload

International Nuclear Information System (INIS)

Kim, Jong Hyun; Seong, Poong Hyun

2002-01-01

This paper proposes a quantitative approach to modeling the information processing of NPP operators. The aim of this work is to derive the amount of the information processed during a certain control task under input information overload. We primarily develop the information processing model having multiple stages, which contains information flow. Then the uncertainty of the information is quantified using the Conant's model, a kind of information theory. We also investigate the applicability of this approach to quantifying the information reduction of operators under the input information overload

Information Processing of Trauma.

Science.gov (United States)

Hartman, Carol R.; Burgess, Ann W.

1993-01-01

This paper presents a neuropsychosocial model of information processing to explain a victimization experience, specifically child sexual abuse. It surveys the relation of sensation, perception, and cognition as a systematic way to provide a framework for studying human behavior and describing human response to traumatic events. (Author/JDD)

Testing an alternate informed consent process.

Science.gov (United States)

Yates, Bernice C; Dodendorf, Diane; Lane, Judy; LaFramboise, Louise; Pozehl, Bunny; Duncan, Kathleen; Knodel, Kendra

2009-01-01

One of the main problems in conducting clinical trials is low participation rate due to potential participants' misunderstanding of the rationale for the clinical trial or perceptions of loss of control over treatment decisions. The objective of this study was to test an alternate informed consent process in cardiac rehabilitation participants that involved the use of a multimedia flip chart to describe a future randomized clinical trial and then asked, hypothetically, if they would participate in the future trial. An attractive and inviting visual presentation of the study was created in the form of a 23-page flip chart that included 24 color photographs displaying information about the purpose of the study, similarities and differences between the two treatment groups, and the data collection process. We tested the flip chart in 35 cardiac rehabilitation participants. Participants were asked if they would participate in this future study on two occasions: immediately after the description of the flip chart and 24 hours later, after reading through the informed consent document. Participants were also asked their perceptions of the flip chart and consent process. Of the 35 participants surveyed, 19 (54%) indicated that they would participate in the future study. No participant changed his or her decision 24 hours later after reading the full consent form. The participation rate improved 145% over that of an earlier feasibility study where the recruitment rate was 22%. Most participants stated that the flip chart was helpful and informative and that the photographs were effective in communicating the purpose of the study. Participation rates could be enhanced in future clinical trials by using a visual presentation to explain and describe the study as part of the informed consent process. More research is needed to test alternate methods of obtaining informed consent.

Occurrence reporting and processing of operations information

International Nuclear Information System (INIS)

1997-01-01

DOE O 232.1A, Occurrence Reporting and Processing of Operations Information, and 10 CFR 830.350, Occurrence Reporting and Processing of Operations Information (when it becomes effective), along with this manual, set forth occurrence reporting requirements for Department of Energy (DOE) Departmental Elements and contractors responsible for the management and operation of DOE-owned and -leased facilities. These requirements include categorization of occurrences related to safety, security, environment, health, or operations (''Reportable Occurrences''); DOE notification of these occurrences; and the development and submission of documented follow-up reports. This Manual provides detailed information for categorizing and reporting occurrences at DOE facilities. Information gathered by the Occurrence Reporting and processing System is used for analysis of the Department's performance in environmental protection, safeguards and security, and safety and health of its workers and the public. This information is also used to develop lessons learned and document events that significantly impact DOE operations

Occurrence reporting and processing of operations information

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-07-21

DOE O 232.1A, Occurrence Reporting and Processing of Operations Information, and 10 CFR 830.350, Occurrence Reporting and Processing of Operations Information (when it becomes effective), along with this manual, set forth occurrence reporting requirements for Department of Energy (DOE) Departmental Elements and contractors responsible for the management and operation of DOE-owned and -leased facilities. These requirements include categorization of occurrences related to safety, security, environment, health, or operations (``Reportable Occurrences``); DOE notification of these occurrences; and the development and submission of documented follow-up reports. This Manual provides detailed information for categorizing and reporting occurrences at DOE facilities. Information gathered by the Occurrence Reporting and processing System is used for analysis of the Department`s performance in environmental protection, safeguards and security, and safety and health of its workers and the public. This information is also used to develop lessons learned and document events that significantly impact DOE operations.

New Product Development (Npd) Process In Subsidiary: Information Perspectives

OpenAIRE

Firmanzah

2008-01-01

Information is an important resource for new product development (NPD) process in subsidiary. However, we still lack of research to analyze NPD process from information perspective in subsidiary context. This research is an exploratory research and it exploited 8 cases of NPD process in consumer goods subsidiaries operating in Indonesian market. Three types of information have been identified and analyzed NPD process; global, regional and local information. The result of this research ...

A simplified computational memory model from information processing.

Science.gov (United States)

Zhang, Lanhua; Zhang, Dongsheng; Deng, Yuqin; Ding, Xiaoqian; Wang, Yan; Tang, Yiyuan; Sun, Baoliang

2016-11-23

This paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At first meta-memory is defined to express the neuron or brain cortices based on the biology and graph theories, and we develop an intra-modular network with the modeling algorithm by mapping the node and edge, and then the bi-modular network is delineated with intra-modular and inter-modular. At last a polynomial retrieval algorithm is introduced. In this paper we simulate the memory phenomena and functions of memorization and strengthening by information processing algorithms. The theoretical analysis and the simulation results show that the model is in accordance with the memory phenomena from information processing view.

Information Processing in Nursing Information Systems: An Evaluation Study from a Developing Country.

Science.gov (United States)

Samadbeik, Mahnaz; Shahrokhi, Nafiseh; Saremian, Marzieh; Garavand, Ali; Birjandi, Mahdi

2017-01-01

In recent years, information technology has been introduced in the nursing departments of many hospitals to support their daily tasks. Nurses are the largest end user group in Hospital Information Systems (HISs). This study was designed to evaluate data processing in the Nursing Information Systems (NISs) utilized in many university hospitals in Iran. This was a cross-sectional study. The population comprised all nurse managers and NIS users of the five training hospitals in Khorramabad city ( N = 71). The nursing subset of HIS-Monitor questionnaire was used to collect the data. Data were analyzed by the descriptive-analytical method and the inductive content analysis. The results indicated that the nurses participating in the study did not take a desirable advantage of paper (2.02) and computerized (2.34) information processing tools to perform nursing tasks. Moreover, the less work experience nurses have, the further they utilize computer tools for processing patient discharge information. The "readability of patient information" and "repetitive and time-consuming documentation" were stated as the most important expectations and problems regarding the HIS by the participating nurses, respectively. The nurses participating in the present study used to utilize paper and computerized information processing tools together to perform nursing practices. Therefore, it is recommended that the nursing process redesign coincides with NIS implementation in the health care centers.

Quantum teleportation for continuous variables and related quantum information processing

International Nuclear Information System (INIS)

Furusawa, Akira; Takei, Nobuyuki

2007-01-01

Quantum teleportation is one of the most important subjects in quantum information science. This is because quantum teleportation can be regarded as not only quantum information transfer but also a building block for universal quantum information processing. Furthermore, deterministic quantum information processing is very important for efficient processing and it can be realized with continuous-variable quantum information processing. In this review, quantum teleportation for continuous variables and related quantum information processing are reviewed from these points of view

Fluctuating Thermodynamics for Biological Processes

Science.gov (United States)

Ham, Sihyun

Because biomolecular processes are largely under thermodynamic control, dynamic extension of thermodynamics is necessary to uncover the mechanisms and driving factors of fluctuating processes. The fluctuating thermodynamics technology presented in this talk offers a practical means for the thermodynamic characterization of conformational dynamics in biomolecules. The use of fluctuating thermodynamics has the potential to provide a comprehensive picture of fluctuating phenomena in diverse biological processes. Through the application of fluctuating thermodynamics, we provide a thermodynamic perspective on the misfolding and aggregation of the various proteins associated with human diseases. In this talk, I will present the detailed concepts and applications of the fluctuating thermodynamics technology for elucidating biological processes. This work was supported by Samsung Science and Technology Foundation under Project Number SSTF-BA1401-13.

Information Processing in Auto-regulated Systems

Directory of Open Access Journals (Sweden)

Karl Javorszky

2003-06-01

Full Text Available Abstract: We present a model of information processing which is based on two concurrent ways of describing the world, where a description in one of the languages limits the possibilities for realisations in the other language. The two describing dimensions appear in our common sense as dichotomies of perspectives: subjective - objective; diversity - similarity; individual - collective. We abstract from the subjective connotations and treat the test theoretical case of an interval on which several concurrent categories can be introduced. We investigate multidimensional partitions as potential carriers of information and compare their efficiency to that of sequenced carriers. We regard the same assembly once as a contemporary collection, once as a longitudinal sequence and find promising inroads towards understanding information processing by auto-regulated systems. Information is understood to point out that what is the case from among alternatives, which could be the case. We have translated these ideas into logical operations on the set of natural numbers and have found two equivalence points on N where matches between sequential and commutative ways of presenting a state of the world can agree in a stable fashion: a flip-flop mechanism is envisioned. By following this new approach, a mathematical treatment of some poignant biomathematical problems is allowed. Also, the concepts presented in this treatise may well have relevance and applications within the information processing and the theory of language fields.

Information Technology Process Improvement Decision-Making: An Exploratory Study from the Perspective of Process Owners and Process Managers

Science.gov (United States)

Lamp, Sandra A.

2012-01-01

There is information available in the literature that discusses information technology (IT) governance and investment decision making from an executive-level perception, yet there is little information available that offers the perspective of process owners and process managers pertaining to their role in IT process improvement and investment…

ATR-FTIR Spectroscopic Evidence for Biomolecular Phosphorus and Carboxyl Groups Facilitating Bacterial Adhesion to Iron Oxides

Science.gov (United States)

Parikh, Sanjai J.; Mukome, Fungai N.D.; Zhang, Xiaoming

2014-01-01

Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy has been used to probe the binding of bacteria to hematite (α-Fe2O3) and goethite (α-FeOOH). In situ ATR-FTIR experiments with bacteria (Pseudomonas putida, P. aeruginosa, Escherichia coli), mixed amino acids, polypeptide extracts, deoxyribonucleic acid (DNA), and a suite of model compounds were conducted. These compounds represent carboxyl, catecholate, amide, and phosphate groups present in siderophores, amino acids, polysaccharides, phospholipids, and DNA. Due in part to the ubiquitous presence of carboxyl groups in biomolecules, numerous IR peaks corresponding to outer-sphere or unbound (1400 cm−1) and inner-sphere (1310-1320 cm−1) coordinated carboxyl groups are noted following reaction of bacteria and biomolecules with α-Fe2O3 and α-FeOOH. However, the data also reveal that the presence of low-level amounts (i.e., 0.45-0.79%) of biomolecular phosphorous groups result in strong IR bands at ~1043 cm−1, corresponding to inner-sphere Fe-O-P bonds, underscoring the importance of bacteria associated P-containing groups in biomolecule and cell adhesion. Spectral comparisons also reveal slightly greater P-O-Fe contributions for bacteria (Pseudomonad, E. coli) deposited on α-FeOOH, as compared to α-Fe2O3. This data demonstrates that slight differences in bacterial adhesion to Fe oxides can be attributed to bacterial species and Fe-oxide minerals. However, more importantly, the strong binding affinity of phosphate in all bacteria samples to both Fe-oxides results in the formation of inner-sphere Fe-O-P bonds, signifying the critical role of biomolecular P in the initiation of bacterial adhesion. PMID:24859052

Zwitterionic Silane Copolymer for Ultra-Stable and Bright Biomolecular Probes Based on Fluorescent Quantum Dot Nanoclusters.

Science.gov (United States)

Dembele, Fatimata; Tasso, Mariana; Trapiella-Alfonso, Laura; Xu, Xiangzhen; Hanafi, Mohamed; Lequeux, Nicolas; Pons, Thomas

2017-05-31

Fluorescent semiconductor quantum dots (QDs) exhibit several unique properties that make them suitable candidates for biomolecular sensing, including high brightness, photostability, broad excitation, and narrow emission spectra. Assembling these QDs into robust and functionalizable nanosized clusters (QD-NSCs) can provide fluorescent probes that are several orders of magnitude brighter than individual QDs, thus allowing an even greater sensitivity of detection with simplified instrumentation. However, the formation of compact, antifouling, functionalizable, and stable QD-NSCs remains a challenging task, especially for a use at ultralow concentrations for single-molecule detection. Here, we describe the development of fluorescent QD-NSCs envisioned as a tool for fast and sensitive biomolecular recognition. First, QDs were assembled into very compact 100-150 nm diameter spherical aggregates; the final QD-NSCs were obtained by growing a cross-linked silica shell around these aggregates. Hydrolytic stability in several concentration and pH conditions is a key requirement for a potential and efficient single-molecule detection tool. However, the hydrolysis of Si-O-Si bonds leads to desorption of monosilane-based surface groups at very low silica concentrations or in a slightly basic medium. Thus, we designed a novel multidentate copolymer composed of multiple silane as well as zwitterionic monomers. Coating silica beads with this multidentate copolymer provided a robust surface chemistry that was demonstrated to be stable against hydrolysis, even at low concentrations. Copolymer-coated silica beads also showed low fouling properties and high colloidal stability in saline solutions. Furthermore, incorporation of additional azido-monomers enabled easy functionalization of QD-NSCs using copper-free bio-orthogonal cyclooctyne-azide click chemistry, as demonstrated by a biotin-streptavidin affinity test.

Cognitive Structures in Vocational Information Processing and Decision Making.

Science.gov (United States)

Nevill, Dorothy D.; And Others

1986-01-01

Tested the assumptions that the structural features of vocational schemas affect vocational information processing and career self-efficacy. Results indicated that effective vocational information processing was facilitated by well-integrated systems that processed information along fewer dimensions. The importance of schematic organization on the…

Expectation, information processing, and subjective duration.

Science.gov (United States)

Simchy-Gross, Rhimmon; Margulis, Elizabeth Hellmuth

2018-01-01

In research on psychological time, it is important to examine the subjective duration of entire stimulus sequences, such as those produced by music (Teki, Frontiers in Neuroscience, 10, 2016). Yet research on the temporal oddball illusion (according to which oddball stimuli seem longer than standard stimuli of the same duration) has examined only the subjective duration of single events contained within sequences, not the subjective duration of sequences themselves. Does the finding that oddballs seem longer than standards translate to entire sequences, such that entire sequences that contain oddballs seem longer than those that do not? Is this potential translation influenced by the mode of information processing-whether people are engaged in direct or indirect temporal processing? Two experiments aimed to answer both questions using different manipulations of information processing. In both experiments, musical sequences either did or did not contain oddballs (auditory sliding tones). To manipulate information processing, we varied the task (Experiment 1), the sequence event structure (Experiments 1 and 2), and the sequence familiarity (Experiment 2) independently within subjects. Overall, in both experiments, the sequences that contained oddballs seemed shorter than those that did not when people were engaged in direct temporal processing, but longer when people were engaged in indirect temporal processing. These findings support the dual-process contingency model of time estimation (Zakay, Attention, Perception & Psychophysics, 54, 656-664, 1993). Theoretical implications for attention-based and memory-based models of time estimation, the pacemaker accumulator and coding efficiency hypotheses of time perception, and dynamic attending theory are discussed.

Mathematics of Information Processing and the Internet

Science.gov (United States)

Hart, Eric W.

2010-01-01

The mathematics of information processing and the Internet can be organized around four fundamental themes: (1) access (finding information easily); (2) security (keeping information confidential); (3) accuracy (ensuring accurate information); and (4) efficiency (data compression). In this article, the author discusses each theme with reference to…

Holledge gauge failure testing using concurrent information processing algorithm

International Nuclear Information System (INIS)

Weeks, G.E.; Daniel, W.E.; Edwards, R.E.; Jannarone, R.J.; Joshi, S.N.; Palakodety, S.S.; Qian, D.

1996-01-01

For several decades, computerized information processing systems and human information processing models have developed with a good deal of mutual influence. Any comprehensive psychology text in this decade uses terms that originated in the computer industry, such as ''cache'' and ''memory'', to describe human information processing. Likewise, many engineers today are using ''artificial intelligence''and ''artificial neural network'' computing tools that originated as models of human thought to solve industrial problems. This paper concerns a recently developed human information processing model, called ''concurrent information processing'' (CIP), and a related set of computing tools for solving industrial problems. The problem of focus is adaptive gauge monitoring; the application is pneumatic pressure repeaters (Holledge gauges) used to measure liquid level and density in the Defense Waste Processing Facility and the Integrated DWPF Melter System

Basic disturbances of information processing in psychosis prediction.

Science.gov (United States)

Bodatsch, Mitja; Klosterkötter, Joachim; Müller, Ralf; Ruhrmann, Stephan

2013-01-01

The basic symptoms (BS) approach provides a valid instrument in predicting psychosis onset and represents moreover a significant heuristic framework for research. The term "basic symptoms" denotes subtle changes of cognition and perception in the earliest and prodromal stages of psychosis development. BS are thought to correspond to disturbances of neural information processing. Following the heuristic implications of the BS approach, the present paper aims at exploring disturbances of information processing, revealed by functional magnetic resonance imaging (fMRI) and electro-encephalographic as characteristics of the at-risk state of psychosis. Furthermore, since high-risk studies employing ultra-high-risk criteria revealed non-conversion rates commonly exceeding 50%, thus warranting approaches that increase specificity, the potential contribution of neural information processing disturbances to psychosis prediction is reviewed. In summary, the at-risk state seems to be associated with information processing disturbances. Moreover, fMRI investigations suggested that disturbances of language processing domains might be a characteristic of the prodromal state. Neurophysiological studies revealed that disturbances of sensory processing may assist psychosis prediction in allowing for a quantification of risk in terms of magnitude and time. The latter finding represents a significant advancement since an estimation of the time to event has not yet been achieved by clinical approaches. Some evidence suggests a close relationship between self-experienced BS and neural information processing. With regard to future research, the relationship between neural information processing disturbances and different clinical risk concepts warrants further investigations. Thereby, a possible time sequence in the prodromal phase might be of particular interest.

ORGANIZATION OF INFORMATION INTERACTION OF AIRPORT PRODUCTION PROCESSES

Directory of Open Access Journals (Sweden)

Yakov Mikhajlovich Dalinger

2017-01-01

Full Text Available The organization of service production attributed to airports activity is analyzed. The importance and the actuality of information interaction problem solution between productive processes as a problem of organization of modern produc- tion are shown.Possibilities and features of information interaction system construction in form of multi-level hierarchical struc- ture have been shown. The airport is considered as an enterprise aimed at service production where it is necessary to analyze much in- formation in a limited time-frame. The production schedule often changes under the influence of many factors. This leads to the increase of the role of computerization and informatization of production processes what predetermines automation of production, creation of information environment and organization of information interaction needed for realization of production processes. The integrated organization form is proposed because it is oriented to the integration of different processes into a universal production system and it allows to conduct the coordination of local goals of particular processes in the context of the global purpose aimed at the improvement of the effectiveness of the airport activity. The main conditions needed for organization of information interaction between production processes and techno- logical operations are considered, and the list of the following problems is determined. The attention is paid to the necessity of compatibility of structure and organization of interaction system in the conditions of the airline and the necessity of be- ing its reflection in the information space of the airline. The usefulness of the intergrated organization form of information interaction based on information exchange between processes and service customers according to the network structure is explained. Multi-level character of this structure confirms its advantage over other items, however it also has a series of features presented

Quantum information processing in nanostructures

International Nuclear Information System (INIS)

Reina Estupinan, John-Henry

2002-01-01

Since information has been regarded os a physical entity, the field of quantum information theory has blossomed. This brings novel applications, such as quantum computation. This field has attracted the attention of numerous researchers with backgrounds ranging from computer science, mathematics and engineering, to the physical sciences. Thus, we now have an interdisciplinary field where great efforts are being made in order to build devices that should allow for the processing of information at a quantum level, and also in the understanding of the complex structure of some physical processes at a more basic level. This thesis is devoted to the theoretical study of structures at the nanometer-scale, 'nanostructures', through physical processes that mainly involve the solid-state and quantum optics, in order to propose reliable schemes for the processing of quantum information. Initially, the main results of quantum information theory and quantum computation are briefly reviewed. Next, the state-of-the-art of quantum dots technology is described. In so doing, the theoretical background and the practicalities required for this thesis are introduced. A discussion of the current quantum hardware used for quantum information processing is given. In particular, the solid-state proposals to date are emphasised. A detailed prescription is given, using an optically-driven coupled quantum dot system, to reliably prepare and manipulate exciton maximally entangled Bell and Greenberger-Horne-Zeilinger (GHZ) states. Manipulation of the strength and duration of selective light-pulses needed for producing these highly entangled states provides us with crucial elements for the processing of solid-state based quantum information. The all-optical generation of states of the so-called Bell basis for a system of two quantum dots (QDs) is exploited for performing the quantum teleportation of the excitonic state of a dot in an array of three coupled QDs. Theoretical predictions suggest

Algorithmic information theory mathematics of digital information processing

CERN Document Server

Seibt, Peter

2007-01-01

Treats the Mathematics of many important areas in digital information processing. This book covers, in a unified presentation, five topics: Data Compression, Cryptography, Sampling (Signal Theory), Error Control Codes, Data Reduction. It is useful for teachers, students and practitioners in Electronic Engineering, Computer Science and Mathematics.

A simplified computational memory model from information processing

Science.gov (United States)

Zhang, Lanhua; Zhang, Dongsheng; Deng, Yuqin; Ding, Xiaoqian; Wang, Yan; Tang, Yiyuan; Sun, Baoliang

2016-01-01

This paper is intended to propose a computational model for memory from the view of information processing. The model, called simplified memory information retrieval network (SMIRN), is a bi-modular hierarchical functional memory network by abstracting memory function and simulating memory information processing. At first meta-memory is defined to express the neuron or brain cortices based on the biology and graph theories, and we develop an intra-modular network with the modeling algorithm by mapping the node and edge, and then the bi-modular network is delineated with intra-modular and inter-modular. At last a polynomial retrieval algorithm is introduced. In this paper we simulate the memory phenomena and functions of memorization and strengthening by information processing algorithms. The theoretical analysis and the simulation results show that the model is in accordance with the memory phenomena from information processing view. PMID:27876847

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Science.gov (United States)

Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

2003-11-01

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

Uma abordagem visual para análise comparativa de redes biomoleculares com apoio de diagramas de Venn

OpenAIRE

Henry Heberle

2014-01-01

Sistemas biológicos podem ser representados por redes que armazenam não apenas informações de conectividade, mas também informações de características de seus nós. No contexto biomolecular, esses nós podem representar proteínas, metabólitos, entre outros tipos de moléculas. Cada molécula possui características anotadas e armazenadas em bases de dados como o Gene Ontology. A comparação visual dessas redes depende de ferramentas que permitam o usuário identificar diferenças e semelhanças entre ...

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

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

Information Systems to Support a Decision Process at Stanford.

Science.gov (United States)

Chaffee, Ellen Earle

1982-01-01

When a rational decision process is desired, information specialists can contribute information and also contribute to the process in which that information is used, thereby promoting rational decision-making. The contribution of Stanford's information specialists to rational decision-making is described. (MLW)

A Petri Net-Based Software Process Model for Developing Process-Oriented Information Systems

Science.gov (United States)

Li, Yu; Oberweis, Andreas

Aiming at increasing flexibility, efficiency, effectiveness, and transparency of information processing and resource deployment in organizations to ensure customer satisfaction and high quality of products and services, process-oriented information systems (POIS) represent a promising realization form of computerized business information systems. Due to the complexity of POIS, explicit and specialized software process models are required to guide POIS development. In this chapter we characterize POIS with an architecture framework and present a Petri net-based software process model tailored for POIS development with consideration of organizational roles. As integrated parts of the software process model, we also introduce XML nets, a variant of high-level Petri nets as basic methodology for business processes modeling, and an XML net-based software toolset providing comprehensive functionalities for POIS development.

Efficiency of cellular information processing

International Nuclear Information System (INIS)

Barato, Andre C; Hartich, David; Seifert, Udo

2014-01-01

We show that a rate of conditional Shannon entropy reduction, characterizing the learning of an internal process about an external process, is bounded by the thermodynamic entropy production. This approach allows for the definition of an informational efficiency that can be used to study cellular information processing. We analyze three models of increasing complexity inspired by the Escherichia coli sensory network, where the external process is an external ligand concentration jumping between two values. We start with a simple model for which ATP must be consumed so that a protein inside the cell can learn about the external concentration. With a second model for a single receptor we show that the rate at which the receptor learns about the external environment can be nonzero even without any dissipation inside the cell since chemical work done by the external process compensates for this learning rate. The third model is more complete, also containing adaptation. For this model we show inter alia that a bacterium in an environment that changes at a very slow time-scale is quite inefficient, dissipating much more than it learns. Using the concept of a coarse-grained learning rate, we show for the model with adaptation that while the activity learns about the external signal the option of changing the methylation level increases the concentration range for which the learning rate is substantial. (paper)

Consciousness: a unique way of processing information.

Science.gov (United States)

Marchetti, Giorgio

2018-02-08

In this article, I argue that consciousness is a unique way of processing information, in that: it produces information, rather than purely transmitting it; the information it produces is meaningful for us; the meaning it has is always individuated. This uniqueness allows us to process information on the basis of our personal needs and ever-changing interactions with the environment, and consequently to act autonomously. Three main basic cognitive processes contribute to realize this unique way of information processing: the self, attention and working memory. The self, which is primarily expressed via the central and peripheral nervous systems, maps our body, the environment, and our relations with the environment. It is the primary means by which the complexity inherent to our composite structure is reduced into the "single voice" of a unique individual. It provides a reference system that (albeit evolving) is sufficiently stable to define the variations that will be used as the raw material for the construction of conscious information. Attention allows for the selection of those variations in the state of the self that are most relevant in the given situation. Attention originates and is deployed from a single locus inside our body, which represents the center of the self, around which all our conscious experiences are organized. Whatever is focused by attention appears in our consciousness as possessing a spatial quality defined by this center and the direction toward which attention is focused. In addition, attention determines two other features of conscious experience: periodicity and phenomenal quality. Self and attention are necessary but not sufficient for conscious information to be produced. Complex forms of conscious experiences, such as the various modes of givenness of conscious experience and the stream of consciousness, need a working memory mechanism to assemble the basic pieces of information selected by attention.

Photonic Architecture for Scalable Quantum Information Processing in Diamond

Directory of Open Access Journals (Sweden)

Kae Nemoto

2014-08-01

Full Text Available Physics and information are intimately connected, and the ultimate information processing devices will be those that harness the principles of quantum mechanics. Many physical systems have been identified as candidates for quantum information processing, but none of them are immune from errors. The challenge remains to find a path from the experiments of today to a reliable and scalable quantum computer. Here, we develop an architecture based on a simple module comprising an optical cavity containing a single negatively charged nitrogen vacancy center in diamond. Modules are connected by photons propagating in a fiber-optical network and collectively used to generate a topological cluster state, a robust substrate for quantum information processing. In principle, all processes in the architecture can be deterministic, but current limitations lead to processes that are probabilistic but heralded. We find that the architecture enables large-scale quantum information processing with existing technology.

The Logic Process Formalism of the Informational Domain

Directory of Open Access Journals (Sweden)

2007-01-01

Full Text Available The performance of present-day informational technologies has two main properties: the universality of the structures used and the flexibility of the final user's interfaces. The first determines the potential cover area of the informational domain. The second determines the diversity and efficiency of processing methods of the proceedings being automated. The mentioned aspects are of great importance in agriculture and ecology because there are complex processes and considerable volumes of used information. For example, the meteoro-logical processes are a part of the ecological one like habitats' existential conditions and are known as a complex prognostic problem. The latter needs considerable computational resources to solve the appropriate equations. Likewise, agriculture as a controlled activity under strong impact from natural conditions has the same high requirements for diverse structures and flexibility of information processing.

Information processing theory in the early design stages

DEFF Research Database (Denmark)

Cash, Philip; Kreye, Melanie

2014-01-01

suggestions for improvements and support. One theory that may be particularly applicable to the early design stages is Information Processing Theory (IPT) as it is linked to the design process with regard to the key concepts considered. IPT states that designers search for information if they perceive......, the new knowledge is shared between the design team to reduce ambiguity with regards to its meaning and to build a shared understanding – reducing perceived uncertainty. Thus, we propose that Information-Processing Theory is suitable to describe designer activity in the early design stages...... uncertainty with regard to the knowledge necessary to solve a design challenge. They then process this information and compare if the new knowledge they have gained covers the previous knowledge gap. In engineering design, uncertainty plays a key role, particularly in the early design stages which has been...

The informed consent process in randomised controlled trials: a nurse-led process.

Science.gov (United States)

Cresswell, Pip; Gilmour, Jean

2014-03-01

Clinical trials are carried out with human participants to answer questions about the best way to diagnose, treat and prevent illness. Participants must give informed consent to take part in clinical trials that requires understanding of how clinical trials work and their purpose. Randomised controlled trials provide strong evidence but their complex design is difficult for both clinicians and participants to understand. Increasingly, ensuring informed consent in randomised controlled trials has become part of the clinical research nurse role. The aim of this study was to explore in depth the clinical research nurse role in the informed consent process using a qualitative descriptive approach. Three clinical research nurses were interviewed and data analysed using a thematic analysis approach. Three themes were identified to describe the process of ensuring informed consent. The first theme, Preparatory partnerships, canvassed the relationships required prior to initiation of the informed consent process. The second theme, Partnering the participant, emphasises the need for ensuring voluntariness and understanding, along with patient advocacy. The third theme, Partnership with the project, highlights the clinical research nurse contribution to the capacity of the trial to answer the research question through appropriate recruiting and follow up of participants. Gaining informed consent in randomised controlled trials was complex and required multiple partnerships. A wide variety of skills was used to protect the safety of trial participants and promote quality research. The information from this study contributes to a greater understanding of the clinical research nurse role, and suggests the informed consent process in trials can be a nurse-led one. In order to gain collegial, employer and industry recognition it is important this aspect of the nursing role is acknowledged.

The minimal work cost of information processing

Science.gov (United States)

Faist, Philippe; Dupuis, Frédéric; Oppenheim, Jonathan; Renner, Renato

2015-07-01

Irreversible information processing cannot be carried out without some inevitable thermodynamical work cost. This fundamental restriction, known as Landauer's principle, is increasingly relevant today, as the energy dissipation of computing devices impedes the development of their performance. Here we determine the minimal work required to carry out any logical process, for instance a computation. It is given by the entropy of the discarded information conditional to the output of the computation. Our formula takes precisely into account the statistically fluctuating work requirement of the logical process. It enables the explicit calculation of practical scenarios, such as computational circuits or quantum measurements. On the conceptual level, our result gives a precise and operational connection between thermodynamic and information entropy, and explains the emergence of the entropy state function in macroscopic thermodynamics.

Information processing and routing in wireless sensor networks

CERN Document Server

Yu, Yang; Krishnamachari, Bhaskar

2006-01-01

This book presents state-of-the-art cross-layer optimization techniques for energy-efficient information processing and routing in wireless sensor networks. Besides providing a survey on this important research area, three specific topics are discussed in detail - information processing in a collocated cluster, information transport over a tree substrate, and information routing for computationally intensive applications. The book covers several important system knobs for cross-layer optimization, including voltage scaling, rate adaptation, and tunable compression. By exploring tradeoffs of en

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

Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.

Science.gov (United States)

Shrot, Yoav; Frydman, Lucio

2011-04-01

A topic of active investigation in 2D NMR relates to the minimum number of scans required for acquiring this kind of spectra, particularly when these are dictated by sampling rather than by sensitivity considerations. Reductions in this minimum number of scans have been achieved by departing from the regular sampling used to monitor the indirect domain, and relying instead on non-uniform sampling and iterative reconstruction algorithms. Alternatively, so-called "ultrafast" methods can compress the minimum number of scans involved in 2D NMR all the way to a minimum number of one, by spatially encoding the indirect domain information and subsequently recovering it via oscillating field gradients. Given ultrafast NMR's simultaneous recording of the indirect- and direct-domain data, this experiment couples the spectral constraints of these orthogonal domains - often calling for the use of strong acquisition gradients and large filter widths to fulfill the desired bandwidth and resolution demands along all spectral dimensions. This study discusses a way to alleviate these demands, and thereby enhance the method's performance and applicability, by combining spatial encoding with iterative reconstruction approaches. Examples of these new principles are given based on the compressed-sensed reconstruction of biomolecular 2D HSQC ultrafast NMR data, an approach that we show enables a decrease of the gradient strengths demanded in this type of experiments by up to 80%. Copyright © 2011 Elsevier Inc. All rights reserved.

Knowledge acquisition process as an issue in information sciences

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Boris Bosančić

2016-07-01

Full Text Available The paper presents an overview of some problems of information science which are explicitly portrayed in literature. It covers the following issues: information explosion, information flood and data deluge, information retrieval and relevance of information, and finally, the problem of scientific communication. The purpose of this paper is to explain why knowledge acquisition, can be considered as an issue in information sciences. The existing theoretical foundation within the information sciences, i.e. the DIKW hierarchy and its key concepts - data, information, knowledge and wisdom, is recognized as a symbolic representation as well as the theoretical foundation of the knowledge acquisition process. Moreover, it seems that the relationship between the DIKW hierarchy and the knowledge acquisition process is essential for a stronger foundation of information sciences in the 'body' of the overall human knowledge. In addition, the history of both the human and machine knowledge acquisition has been considered, as well as a proposal that the DIKW hierarchy take place as a symbol of general knowledge acquisition process, which could equally relate to both human and machine knowledge acquisition. To achieve this goal, it is necessary to modify the existing concept of the DIKW hierarchy. The appropriate modification of the DIKW hierarchy (one of which is presented in this paper could result in a much more solid theoretical foundation of the knowledge acquisition process and information sciences as a whole. The theoretical assumptions on which the knowledge acquisition process may be established as a problem of information science are presented at the end of the paper. The knowledge acquisition process does not necessarily have to be the subject of epistemology. It may establish a stronger link between the concepts of data and knowledge; furthermore, it can be used in the context of scientific research, but on the more primitive level than conducting

Classicality of quantum information processing

International Nuclear Information System (INIS)

Poulin, David

2002-01-01

The ultimate goal of the classicality program is to quantify the amount of quantumness of certain processes. Here, classicality is studied for a restricted type of process: quantum information processing (QIP). Under special conditions, one can force some qubits of a quantum computer into a classical state without affecting the outcome of the computation. The minimal set of conditions is described and its structure is studied. Some implications of this formalism are the increase of noise robustness, a proof of the quantumness of mixed state quantum computing, and a step forward in understanding the very foundation of QIP

On the Concept of Information and Its Role in Nature

Directory of Open Access Journals (Sweden)

Juan G. Roederer

2003-02-01

and do not require any operations of information processing. Information only enters the non-living physical world when a living thing interacts with it-and when a scientist extracts information through observation and measurement. But for living organisms, information is the very essence of their existence: to maintain a long-term state of unstable thermodynamic equilibrium with its surroundings, consistently increase its organization and reproduce, an organism has to rely on information-based interactions in which form or pattern, not energy, is the controlling factor. This latter class comprises biomolecular information processes controlling the metabolism, growth, multiplication and differentiation of cells, and neural information processes controlling animal behavior and intelligence. The only way new information can appear is through the process of biological evolution and, in the short term, through sensory acquisition and the manipulation of images in the nervous system. Non-living informational systems such as books, computers, AI systems and other artifacts, as well as living organisms that are the result of breeding or cloning, are planned by human beings and will not be considered here.

On the concept of information and its role in nature

International Nuclear Information System (INIS)

Roederer, Juan G.

2002-09-01

-living physical world when a living thing interacts with it - and when a scientist extracts information through observation and measurement. But for living organisms, information is the very essence of their existence: to maintain a long-term state of unstable thermodynamic equilibrium with its surroundings, consistently increase its organization and reproduce, an organism has to rely on information-based interactions. This latter class comprises biomolecular information processes controlling the metabolism, growth, multiplication and differentiation of cells, and neural information processes controlling animal behavior and intelligence. The only way new information can appear is through the process of biological evolution and, in the short term, through sensory acquisition and the manipulation of images in the nervous system. Non-living informational systems such as books, computers, Al systems and other artifacts, as well as living organisms that are the result of breeding or cloning, are planned by human beings and will not be considered here. (author)

On the Concept of Information and Its Role in Nature

Science.gov (United States)

Roederer, Juan G.

2003-03-01

operations of information processing. Information only enters the non-living physical world when a living thing interacts with it-and when a scientist extracts information through observation and measurement. But for living organisms, information is the very essence of their existence: to maintain a long-term state of unstable thermodynamic equilibrium with its surroundings, consistently increase its organization and reproduce, an organism has to rely on information-based interactions in which form or pattern, not energy, is the controlling factor. This latter class comprises biomolecular information processes controlling the metabolism, growth, multiplication and differentiation of cells, and neural information processes controlling animal behavior and intelligence. The only way new information can appear is through the process of biological evolution and, in the short term, through sensory acquisition and the manipulation of images in the nervous system. Non-living informational systems such as books, computers, AI systems and other artifacts, as well as living organisms that are the result of breeding or cloning, are planned by human beings and will not be considered here.

Theoretical aspects of cellular decision-making and information-processing.

Science.gov (United States)

Kobayashi, Tetsuya J; Kamimura, Atsushi

2012-01-01

Microscopic biological processes have extraordinary complexity and variety at the sub-cellular, intra-cellular, and multi-cellular levels. In dealing with such complex phenomena, conceptual and theoretical frameworks are crucial, which enable us to understand seemingly different intra- and inter-cellular phenomena from unified viewpoints. Decision-making is one such concept that has attracted much attention recently. Since a number of cellular behavior can be regarded as processes to make specific actions in response to external stimuli, decision-making can cover and has been used to explain a broad range of different cellular phenomena [Balázsi et al. (Cell 144(6):910, 2011), Zeng et al. (Cell 141(4):682, 2010)]. Decision-making is also closely related to cellular information-processing because appropriate decisions cannot be made without exploiting the information that the external stimuli contain. Efficiency of information transduction and processing by intra-cellular networks determines the amount of information obtained, which in turn limits the efficiency of subsequent decision-making. Furthermore, information-processing itself can serve as another concept that is crucial for understanding of other biological processes than decision-making. In this work, we review recent theoretical developments on cellular decision-making and information-processing by focusing on the relation between these two concepts.

Career information processing strategies of secondary school ...

African Journals Online (AJOL)

This study examined the strategies commonly adopted by Osun state secondary school students in processing career information. It specifically examined the sources of career information available to the students, the uses to which the students put the information collected and how their career decision making skills can be ...

Attachment in Middle Childhood: Associations with Information Processing

Science.gov (United States)

Zimmermann, Peter; Iwanski, Alexandra

2015-01-01

Attachment theory suggests that internal working models of self and significant others influence adjustment during development by controlling information processing and self-regulation. We provide a conceptual overview on possible mechanisms linking attachment and information processing and review the current literature in middle childhood.…

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.

Science.gov (United States)

Prinz, Jan-Hendrik; Chodera, John D; Pande, Vijay S; Swope, William C; Smith, Jeremy C; Noé, Frank

2011-06-28

Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.

Process system of radiometric and magnetometric aerial information

International Nuclear Information System (INIS)

Bazua Rueda, L.F.

1985-01-01

The author has been working first in the National Institute of Nuclear Energy (Mexico) and then in URAMEX (Uranio Mexicano) since 1975 to 1983, integrated to radiometric and magnetometric aerial prospecting projects in computerized processing of information aspects. During this period the author participated in the work out of computing systems, information processing and mathematical procedures definition for the geophysical reduction of the calibration equipment data. With cumulated experience, in this thesis are presented aspects concerning to management and operation of computerized processing of information systems. Operation handbooks of the majority of modules are presented. Program lists are not included. (Author)

Single-Cell Biomolecular Analysis of Coral Algal Symbionts Reveals Opposing Metabolic Responses to Heat Stress and Expulsion

Directory of Open Access Journals (Sweden)

Katherina Petrou

2018-03-01

Full Text Available The success of corals in nutrient poor environments is largely attributed to the symbiosis between the cnidarian host and its intracellular alga. Warm water anomalies have been shown to destabilize this symbiosis, yet detailed analysis of the effect of temperature and expulsion on cell-specific carbon and nutrient allocation in the symbiont is limited. Here, we exposed colonies of the hard coral Acropora millepora to heat stress and using synchrotron-based infrared microspectroscopy measured the biomolecular profiles of individual in hospite and expelled symbiont cells at an acute state of bleaching. Our results showed symbiont metabolic profiles to be remarkably distinct with heat stress and expulsion, where the two effectors elicited opposing metabolic adjustments independent of treatment or cell type. Elevated temperature resulted in biomolecular changes reflecting cellular stress, with relative increases in free amino acids and phosphorylation of molecules and a concomitant decline in protein content, suggesting protein modification and degradation. This contrasted with the metabolic profiles of expelled symbionts, which showed relative decreases in free amino acids and phosphorylated molecules, but increases in proteins and lipids, suggesting expulsion lessens the overall effect of heat stress on the metabolic signature of the algal symbionts. Interestingly, the combined effects of expulsion and thermal stress were additive, reducing the overall shifts in all biomolecules, with the notable exception of the significant accumulation of lipids and saturated fatty acids. This first use of a single-cell metabolomics approach on the coral symbiosis provides novel insight into coral bleaching and emphasizes the importance of a single-cell approach to demark the cell-to-cell variability in the physiology of coral cellular populations.

Setting a new paradigm in cognitive science information: contributions to the process of knowing the information professional

Directory of Open Access Journals (Sweden)

Paula Regina Dal' Evedove

2013-05-01

Full Text Available Introduction: Studies about human cognition represent a relevant perspective in information science, considering the subjective actions of information professionals and dialogic process that should permeate the activity of subjects dealing with the organization and representation of information.Objective: Explore the approach of the cognitive perspective in information science and their new settings by contemporary needs of information to reflect on the process of meeting the professional information through the social reality that permeates the contexts of information.Methodology: Reflection on theoretical aspects that deal with the cognitive development to discuss the implications of the cognitive approach in information science and its evolution in the scope of the representation and processing of information.Results: Research in Information Science must consider issues of cognitive and social order that underlie information processing and the process of knowing the information professional as knowledge structures must be explained from the social context of knowing subjects.Conclusions: There is a need to investigate the process of knowing the information professional in the bias of socio-cognitive approach, targeting new elements for the understanding of the relationship information (cognitive manifestations and its implications on the social dimension.

Using life cycle information in process discovery

NARCIS (Netherlands)

Leemans, S.J.J.; Fahland, D.; Van Der Aalst, W.M.P.; Reichert, M.; Reijers, H.A.

2016-01-01

Understanding the performance of business processes is an important part of any business process intelligence project. From historical information recorded in event logs, performance can be measured and visualized on a discovered process model. Thereby the accuracy of the measured performance, e.g.,

Influence Business Process On The Quality Of Accounting Information System

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Meiryani

2015-01-01

Full Text Available Abstract The purpose of this study was to determine the influence of business process to the quality of the accounting information system. This study aims to examine the influence of business process on the quality of the information system of accounting information system. The study was theoritical research which considered the roles of business process on quality of accounting information system which use secondary data collection. The results showed that the business process have a significant effect on the quality of accounting information systems.

Information processing for aerospace structural health monitoring

Science.gov (United States)

Lichtenwalner, Peter F.; White, Edward V.; Baumann, Erwin W.

1998-06-01

Structural health monitoring (SHM) technology provides a means to significantly reduce life cycle of aerospace vehicles by eliminating unnecessary inspections, minimizing inspection complexity, and providing accurate diagnostics and prognostics to support vehicle life extension. In order to accomplish this, a comprehensive SHM system will need to acquire data from a wide variety of diverse sensors including strain gages, accelerometers, acoustic emission sensors, crack growth gages, corrosion sensors, and piezoelectric transducers. Significant amounts of computer processing will then be required to convert this raw sensor data into meaningful information which indicates both the diagnostics of the current structural integrity as well as the prognostics necessary for planning and managing the future health of the structure in a cost effective manner. This paper provides a description of the key types of information processing technologies required in an effective SHM system. These include artificial intelligence techniques such as neural networks, expert systems, and fuzzy logic for nonlinear modeling, pattern recognition, and complex decision making; signal processing techniques such as Fourier and wavelet transforms for spectral analysis and feature extraction; statistical algorithms for optimal detection, estimation, prediction, and fusion; and a wide variety of other algorithms for data analysis and visualization. The intent of this paper is to provide an overview of the role of information processing for SHM, discuss various technologies which can contribute to accomplishing this role, and present some example applications of information processing for SHM implemented at the Boeing Company.

Advanced information processing system

Science.gov (United States)

Lala, J. H.

1984-01-01

Design and performance details of the advanced information processing system (AIPS) for fault and damage tolerant data processing on aircraft and spacecraft are presented. AIPS comprises several computers distributed throughout the vehicle and linked by a damage tolerant data bus. Most I/O functions are available to all the computers, which run in a TDMA mode. Each computer performs separate specific tasks in normal operation and assumes other tasks in degraded modes. Redundant software assures that all fault monitoring, logging and reporting are automated, together with control functions. Redundant duplex links and damage-spread limitation provide the fault tolerance. Details of an advanced design of a laboratory-scale proof-of-concept system are described, including functional operations.

Understanding the Information Research Process of Experienced Online Information Researchers to Inform Development of a Scholars Portal

Directory of Open Access Journals (Sweden)

Martha Whitehead

2009-06-01

Full Text Available Objective - The main purpose of this study was to understand the information research process of experienced online information researchers in a variety of disciplines, gather their ideas for improvement and as part of this to validate a proposed research framework for use in future development of Ontario’s Scholars Portal.Methods - This was a qualitative research study in which sixty experienced online information researchers participated in face-to-face workshops that included a collaborative design component. The sessions were conducted and recorded by usability specialists who subsequently analyzed the data and identified patterns and themes.Results - Key themes included the similarities of the information research process across all disciplines, the impact of interdisciplinarity, the social aspect of research and opportunities for process improvement. There were many specific observations regarding current and ideal processes. Implications for portal development and further research included: supporting a common process while accommodating user-defined differences; supporting citation chaining practices with new opportunities for data linkage and granularity; enhancing keyword searching with various types of intervention; exploring trusted social networks; exploring new mental models for data manipulation while retaining traditional objects; improving citation and document management. Conclusion – The majority of researchers in the study had almost no routine in their information research processes, had developed few techniques to assist themselves and had very little awareness of the tools available to help them. There are many opportunities to aid researchers in the research process that can be explored when developing scholarly research portals. That development will be well guided by the framework ‘discover, gather, synthesize, create, share.’

Information processing in the vertebrate habenula.

Science.gov (United States)

Fore, Stephanie; Palumbo, Fabrizio; Pelgrims, Robbrecht; Yaksi, Emre

2018-06-01

The habenula is a brain region that has gained increasing popularity over the recent years due to its role in processing value-related and experience-dependent information with a strong link to depression, addiction, sleep and social interactions. This small diencephalic nucleus is proposed to act as a multimodal hub or a switchboard, where inputs from different brain regions converge. These diverse inputs to the habenula carry information about the sensory world and the animal's internal state, such as reward expectation or mood. However, it is not clear how these diverse habenular inputs interact with each other and how such interactions contribute to the function of habenular circuits in regulating behavioral responses in various tasks and contexts. In this review, we aim to discuss how information processing in habenular circuits, can contribute to specific behavioral programs that are attributed to the habenula. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Process Model for Goal-Based Information Retrieval

Directory of Open Access Journals (Sweden)

Harvey Hyman

2014-12-01

Full Text Available In this paper we examine the domain of information search and propose a "goal-based" approach to study search strategy. We describe "goal-based information search" using a framework of Knowledge Discovery. We identify two Information Retrieval (IR goals using the constructs of Knowledge Acquisition (KA and Knowledge Explanation (KE. We classify these constructs into two specific information problems: An exploration-exploitation problem and an implicit-explicit problem. Our proposed framework is an extension of prior work in this domain, applying an IR Process Model originally developed for Legal-IR and adapted to Medical-IR. The approach in this paper is guided by the recent ACM-SIG Medical Information Retrieval (MedIR Workshop definition: "methodologies and technologies that seek to improve access to medical information archives via a process of information retrieval."

Quantum information processing with trapped ions

International Nuclear Information System (INIS)

Haeffner, H.; Haensel, W.; Rapol, U.; Koerber, T.; Benhelm, J.; Riebe, M.; Chek-al-Kar, D.; Schmidt-Kaler, F.; Becher, C.; Roos, C.; Blatt, R.

2005-01-01

Single Ca + ions and crystals of Ca + ions are confined in a linear Paul trap and are investigated for quantum information processing. Here we report on recent experimental advancements towards a quantum computer with such a system. Laser-cooled trapped ions are ideally suited systems for the investigation and implementation of quantum information processing as one can gain almost complete control over their internal and external degrees of freedom. The combination of a Paul type ion trap with laser cooling leads to unique properties of trapped cold ions, such as control of the motional state down to the zero-point of the trapping potential, a high degree of isolation from the environment and thus a very long time available for manipulations and interactions at the quantum level. The very same properties make single trapped atoms and ions well suited for storing quantum information in long lived internal states, e.g. by encoding a quantum bit (qubit) of information within the coherent superposition of the S 1/2 ground state and the metastable D 5/2 excited state of Ca + . Recently we have achieved the implementation of simple algorithms with up to 3 qubits on an ion-trap quantum computer. We will report on methods to implement single qubit rotations, the realization of a two-qubit universal quantum gate (Cirac-Zoller CNOT-gate), the deterministic generation of multi-particle entangled states (GHZ- and W-states), their full tomographic reconstruction, the realization of deterministic quantum teleportation, its quantum process tomography and the encoding of quantum information in decoherence-free subspaces with coherence times exceeding 20 seconds. (author)

Horizontal information drives the behavioural signatures of face processing

Directory of Open Access Journals (Sweden)

Valerie Goffaux

2010-09-01

Full Text Available Recent psychophysical evidence indicates that the vertical arrangement of horizontal information is particularly important for encoding facial identity. In this paper we extend this notion to examine the role that information at different (particularly cardinal orientations might play in a number of established phenomena each a behavioural “signature” of face processing. In particular we consider (a the face inversion effect (FIE, (b the facial identity after-effect, (c face-matching across viewpoint, and (d interactive, so-called holistic, processing of face parts. We report that filtering faces to remove all but the horizontal information largely preserves these effects but conversely, retaining vertical information generally diminishes or abolishes them. We conclude that preferential processing of horizontal information is a central feature of human face processing that supports many of the behavioural signatures of this critical visual operation.

Influence Business Process On The Quality Of Accounting Information System

OpenAIRE

Meiryani; Muhammad Syaifullah

2015-01-01

Abstract The purpose of this study was to determine the influence of business process to the quality of the accounting information system. This study aims to examine the influence of business process on the quality of the information system of accounting information system. The study was theoritical research which considered the roles of business process on quality of accounting information system which use secondary data collection. The results showed that the business process have a signifi...

Information Processing Capacity of Dynamical Systems

Science.gov (United States)

Dambre, Joni; Verstraeten, David; Schrauwen, Benjamin; Massar, Serge

2012-07-01

Many dynamical systems, both natural and artificial, are stimulated by time dependent external signals, somehow processing the information contained therein. We demonstrate how to quantify the different modes in which information can be processed by such systems and combine them to define the computational capacity of a dynamical system. This is bounded by the number of linearly independent state variables of the dynamical system, equaling it if the system obeys the fading memory condition. It can be interpreted as the total number of linearly independent functions of its stimuli the system can compute. Our theory combines concepts from machine learning (reservoir computing), system modeling, stochastic processes, and functional analysis. We illustrate our theory by numerical simulations for the logistic map, a recurrent neural network, and a two-dimensional reaction diffusion system, uncovering universal trade-offs between the non-linearity of the computation and the system's short-term memory.

Information Processing Capacity of Dynamical Systems

Science.gov (United States)

Dambre, Joni; Verstraeten, David; Schrauwen, Benjamin; Massar, Serge

2012-01-01

Many dynamical systems, both natural and artificial, are stimulated by time dependent external signals, somehow processing the information contained therein. We demonstrate how to quantify the different modes in which information can be processed by such systems and combine them to define the computational capacity of a dynamical system. This is bounded by the number of linearly independent state variables of the dynamical system, equaling it if the system obeys the fading memory condition. It can be interpreted as the total number of linearly independent functions of its stimuli the system can compute. Our theory combines concepts from machine learning (reservoir computing), system modeling, stochastic processes, and functional analysis. We illustrate our theory by numerical simulations for the logistic map, a recurrent neural network, and a two-dimensional reaction diffusion system, uncovering universal trade-offs between the non-linearity of the computation and the system's short-term memory. PMID:22816038

Attachment affects social information processing: Specific electrophysiological effects of maternal stimuli.

Science.gov (United States)

Wu, Lili; Gu, Ruolei; Zhang, Jianxin

2016-01-01

Attachment is critical to each individual. It affects the cognitive-affective processing of social information. The present study examines how attachment affects the processing of social information, specifically maternal information. We assessed the behavioral and electrophysiological responses to maternal information (compared to non-specific others) in a Go/No-go Association Task (GNAT) with 22 participants. The results illustrated that attachment affected maternal information processing during three sequential stages of information processing. First, attachment affected visual perception, reflected by enhanced P100 and N170 elicited by maternal information as compared to others information. Second, compared to others, mother obtained more attentional resources, reflected by faster behavioral response to maternal information and larger P200 and P300. Finally, mother was evaluated positively, reflected by shorter P300 latency in a mother + good condition as compared to a mother + bad condition. These findings indicated that the processing of attachment-relevant information is neurologically differentiated from other types of social information from an early stage of perceptual processing to late high-level processing.

Principles of neural information processing

CERN Document Server

Seelen, Werner v

2016-01-01

In this fundamental book the authors devise a framework that describes the working of the brain as a whole. It presents a comprehensive introduction to the principles of Neural Information Processing as well as recent and authoritative research. The books´ guiding principles are the main purpose of neural activity, namely, to organize behavior to ensure survival, as well as the understanding of the evolutionary genesis of the brain. Among the developed principles and strategies belong self-organization of neural systems, flexibility, the active interpretation of the world by means of construction and prediction as well as their embedding into the world, all of which form the framework of the presented description. Since, in brains, their partial self-organization, the lifelong adaptation and their use of various methods of processing incoming information are all interconnected, the authors have chosen not only neurobiology and evolution theory as a basis for the elaboration of such a framework, but also syst...

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.

Science.gov (United States)

Qi, Ruxi; Botello-Smith, Wesley M; Luo, Ray

2017-07-11

Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes. Though great efforts have been put into developing efficient PBE numerical models, challenges still remain due to the high dimensionality of typical biomolecular systems. In this study, we implemented and analyzed commonly used linear PBE solvers for the ever-improving graphics processing units (GPU) for biomolecular simulations, including both standard and preconditioned conjugate gradient (CG) solvers with several alternative preconditioners. Our implementation utilizes the standard Nvidia CUDA libraries cuSPARSE, cuBLAS, and CUSP. Extensive tests show that good numerical accuracy can be achieved given that the single precision is often used for numerical applications on GPU platforms. The optimal GPU performance was observed with the Jacobi-preconditioned CG solver, with a significant speedup over standard CG solver on CPU in our diversified test cases. Our analysis further shows that different matrix storage formats also considerably affect the efficiency of different linear PBE solvers on GPU, with the diagonal format best suited for our standard finite-difference linear systems. Further efficiency may be possible with matrix-free operations and integrated grid stencil setup specifically tailored for the banded matrices in PBE-specific linear systems.

Living is information processing: from molecules to global systems

OpenAIRE

Farnsworth, Keith D.; Nelson, John; Gershenson, Carlos

2012-01-01

We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; (b) this information processing has one overall function - to perpetuate itself; and (c) the processing method is filtration (cognition) of, and synthesis of, info...

RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

Science.gov (United States)

Guan, W.; Cheng, X.; Huang, J.; Huber, G.; Li, W.; McCammon, J. A.; Zhang, B.

2018-06-01

RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) (Greengard and Rokhlin, 1997) where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library (DeBuhr et al., 2016, 2018). Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12,288 cores, while achieving approximately 54% strong-scaling efficiency.

Development of time sensitivity and information processing speed.

Directory of Open Access Journals (Sweden)

Sylvie Droit-Volet

Full Text Available The aim of this study was to examine whether age-related changes in the speed of information processing are the best predictors of the increase in sensitivity to time throughout childhood. Children aged 5 and 8 years old, as well adults, were given two temporal bisection tasks, one with short (0.5/1-s and the other with longer (4/8-s anchor durations. In addition, the participants' scores on different neuropsychological tests assessing both information processing speed and other dimensions of cognitive control (short-term memory, working memory, selective attention were calculated. The results showed that the best predictor of individual variances in sensitivity to time was information processing speed, although working memory also accounted for some of the individual differences in time sensitivity, albeit to a lesser extent. In sum, the faster the information processing speed of the participants, the higher their sensitivity to time was. These results are discussed in the light of the idea that the development of temporal capacities has its roots in the maturation of the dynamic functioning of the brain.

Splash, pop, sizzle: Information processing with phononic computing

Directory of Open Access Journals (Sweden)

Sophia R. Sklan

2015-05-01

Full Text Available Phonons, the quanta of mechanical vibration, are important to the transport of heat and sound in solid materials. Recent advances in the fundamental control of phonons (phononics have brought into prominence the potential role of phonons in information processing. In this review, the many directions of realizing phononic computing and information processing are examined. Given the relative similarity of vibrational transport at different length scales, the related fields of acoustic, phononic, and thermal information processing are all included, as are quantum and classical computer implementations. Connections are made between the fundamental questions in phonon transport and phononic control and the device level approach to diodes, transistors, memory, and logic.

Information processing in the CNS: a supramolecular chemistry?

Science.gov (United States)

Tozzi, Arturo

2015-10-01

How does central nervous system process information? Current theories are based on two tenets: (a) information is transmitted by action potentials, the language by which neurons communicate with each other-and (b) homogeneous neuronal assemblies of cortical circuits operate on these neuronal messages where the operations are characterized by the intrinsic connectivity among neuronal populations. In this view, the size and time course of any spike is stereotypic and the information is restricted to the temporal sequence of the spikes; namely, the "neural code". However, an increasing amount of novel data point towards an alternative hypothesis: (a) the role of neural code in information processing is overemphasized. Instead of simply passing messages, action potentials play a role in dynamic coordination at multiple spatial and temporal scales, establishing network interactions across several levels of a hierarchical modular architecture, modulating and regulating the propagation of neuronal messages. (b) Information is processed at all levels of neuronal infrastructure from macromolecules to population dynamics. For example, intra-neuronal (changes in protein conformation, concentration and synthesis) and extra-neuronal factors (extracellular proteolysis, substrate patterning, myelin plasticity, microbes, metabolic status) can have a profound effect on neuronal computations. This means molecular message passing may have cognitive connotations. This essay introduces the concept of "supramolecular chemistry", involving the storage of information at the molecular level and its retrieval, transfer and processing at the supramolecular level, through transitory non-covalent molecular processes that are self-organized, self-assembled and dynamic. Finally, we note that the cortex comprises extremely heterogeneous cells, with distinct regional variations, macromolecular assembly, receptor repertoire and intrinsic microcircuitry. This suggests that every neuron (or group of

Knowledge environments representing molecular entities for the virtual physiological human.

Science.gov (United States)

Hofmann-Apitius, Martin; Fluck, Juliane; Furlong, Laura; Fornes, Oriol; Kolárik, Corinna; Hanser, Susanne; Boeker, Martin; Schulz, Stefan; Sanz, Ferran; Klinger, Roman; Mevissen, Theo; Gattermayer, Tobias; Oliva, Baldo; Friedrich, Christoph M

2008-09-13

In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to complex organ function. The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly. Here, we describe methods and strategies to generate knowledge environments representing molecular entities that can be used for modelling the molecular scale of the VPH. Our strategy to generate knowledge environments representing molecular entities is based on the combination of information extraction from scientific text and the integration of information from biomolecular databases. We introduce @neuLink, a first prototype of an automatically generated, disease-specific knowledge environment combining biomolecular, chemical, genetic and medical information. Finally, we provide a perspective for the future implementation and use of knowledge environments representing molecular entities for the VPH.

Advances in intelligent process-aware information systems concepts, methods, and technologies

CERN Document Server

Oberhauser, Roy; Reichert, Manfred

2017-01-01

This book provides a state-of-the-art perspective on intelligent process-aware information systems and presents chapters on specific facets and approaches applicable to such systems. Further, it highlights novel advances and developments in various aspects of intelligent process-aware information systems and business process management systems. Intelligence capabilities are increasingly being integrated into or created in many of today’s software products and services. Process-aware information systems provide critical computing infrastructure to support the various processes involved in the creation and delivery of business products and services. Yet the integration of intelligence capabilities into process-aware information systems is a non-trivial yet necessary evolution of these complex systems. The book’s individual chapters address adaptive process management, case management processes, autonomically-capable processes, process-oriented information logistics, process recommendations, reasoning over ...

Selective exposure to information: how different modes of decision making affect subsequent confirmatory information processing.

Science.gov (United States)

Fischer, Peter; Fischer, Julia; Weisweiler, Silke; Frey, Dieter

2010-12-01

We investigated whether different modes of decision making (deliberate, intuitive, distracted) affect subsequent confirmatory processing of decision-consistent and inconsistent information. Participants showed higher levels of confirmatory information processing when they made a deliberate or an intuitive decision versus a decision under distraction (Studies 1 and 2). As soon as participants have a cognitive (i.e., deliberate cognitive analysis) or affective (i.e., intuitive and gut feeling) reason for their decision, the subjective confidence in the validity of their decision increases, which results in increased levels of confirmatory information processing (Study 2). In contrast, when participants are distracted during decision making, they are less certain about the validity of their decision and thus are subsequently more balanced in the processing of decision-relevant information.

10 CFR 1017.28 - Processing on Automated Information Systems (AIS).

Science.gov (United States)

2010-01-01

... 10 Energy 4 2010-01-01 2010-01-01 false Processing on Automated Information Systems (AIS). 1017.28... UNCLASSIFIED CONTROLLED NUCLEAR INFORMATION Physical Protection Requirements § 1017.28 Processing on Automated Information Systems (AIS). UCNI may be processed or produced on any AIS that complies with the guidance in OMB...

ENERGETIC CHARGE OF AN INFORMATION PROCESS

Directory of Open Access Journals (Sweden)

Popova T.M.

2009-12-01

Full Text Available Main laws of technical thermodynamics are universal and could be applied to processes other than thermodynamic ones. The results of the comparison of peculiarities of irreversible informational and thermodynamic processes are presented in the article and a new term “Infopy” is used. A more precise definition of “infopy” as an energetic charge is given in the article.

On the fragmentation of process information : challenges, solutions, and outlook

NARCIS (Netherlands)

Aa, van der J.H.; Leopold, H.; Mannhardt, F.; Reijers, H.A.; Gaaloul, K.; Schmidt, R.; Nurcan, S.; Guerreiro, S.; Ma, Q.

2015-01-01

An organization’s knowledge on its business processes represents valuable corporate knowledge because it can be used to enhance the performance of these processes. In many organizations, documentation of process knowledge is scattered around various process information sources. Such information

Supporting risk-informed decisions during business process execution

NARCIS (Netherlands)

Conforti, R.; Leoni, de M.; La Rosa, M.; Aalst, van der W.M.P.; Salinesi, C.; Norrie, M.C.; Pastor, O.

2013-01-01

This paper proposes a technique that supports process participants in making risk-informed decisions, with the aim to reduce the process risks. Risk reduction involves decreasing the likelihood and severity of a process fault from occurring. Given a process exposed to risks, e.g. a financial process

[Information processing speed and influential factors in multiple sclerosis].

Science.gov (United States)

Zhang, M L; Xu, E H; Dong, H Q; Zhang, J W

2016-04-19

To study the information processing speed and the influential factors in multiple sclerosis (MS) patients. A total of 36 patients with relapsing-remitting MS (RRMS), 21 patients with secondary progressive MS (SPMS), and 50 healthy control subjects from Xuanwu Hospital of Capital Medical University between April 2010 and April 2012 were included into this cross-sectional study.Neuropsychological tests was conducted after the disease had been stable for 8 weeks, including information processing speed, memory, executive functions, language and visual perception.Correlation between information processing speed and depression, fatigue, Expanded Disability Status Scale (EDSS) were studied. (1)MS patient groups demonstrated cognitive deficits compared to healthy controls.The Symbol Digit Modalities Test (SDMT) (control group 57±12; RRMS group 46±17; SPMS group 35±10, Pinformation processing (Pinformation processing speed, verbal memory and executive functioning are seen in MS patients, especially in SPMS subtype, while visual-spatial function is relatively reserved.Age, white matter change scales, EDSS scores, depression are negatively associated with information processing speed.

Unveiling the mystery of visual information processing in human brain.

Science.gov (United States)

Diamant, Emanuel

2008-08-15

It is generally accepted that human vision is an extremely powerful information processing system that facilitates our interaction with the surrounding world. However, despite extended and extensive research efforts, which encompass many exploration fields, the underlying fundamentals and operational principles of visual information processing in human brain remain unknown. We still are unable to figure out where and how along the path from eyes to the cortex the sensory input perceived by the retina is converted into a meaningful object representation, which can be consciously manipulated by the brain. Studying the vast literature considering the various aspects of brain information processing, I was surprised to learn that the respected scholarly discussion is totally indifferent to the basic keynote question: "What is information?" in general or "What is visual information?" in particular. In the old days, it was assumed that any scientific research approach has first to define its basic departure points. Why was it overlooked in brain information processing research remains a conundrum. In this paper, I am trying to find a remedy for this bizarre situation. I propose an uncommon definition of "information", which can be derived from Kolmogorov's Complexity Theory and Chaitin's notion of Algorithmic Information. Embracing this new definition leads to an inevitable revision of traditional dogmas that shape the state of the art of brain information processing research. I hope this revision would better serve the challenging goal of human visual information processing modeling.

An analytical approach to customer requirement information processing

Science.gov (United States)

Zhou, Zude; Xiao, Zheng; Liu, Quan; Ai, Qingsong

2013-11-01

'Customer requirements' (CRs) management is a key component of customer relationship management (CRM). By processing customer-focused information, CRs management plays an important role in enterprise systems (ESs). Although two main CRs analysis methods, quality function deployment (QFD) and Kano model, have been applied to many fields by many enterprises in the past several decades, the limitations such as complex processes and operations make them unsuitable for online businesses among small- and medium-sized enterprises (SMEs). Currently, most SMEs do not have the resources to implement QFD or Kano model. In this article, we propose a method named customer requirement information (CRI), which provides a simpler and easier way for SMEs to run CRs analysis. The proposed method analyses CRs from the perspective of information and applies mathematical methods to the analysis process. A detailed description of CRI's acquisition, classification and processing is provided.

Mental Status Documentation: Information Quality and Data Processes.

Science.gov (United States)

Weir, Charlene; Gibson, Bryan; Taft, Teresa; Slager, Stacey; Lewis, Lacey; Staggers, Nancy

2016-01-01

Delirium is a fluctuating disturbance of cognition and/or consciousness associated with poor outcomes. Caring for patients with delirium requires integration of disparate information across clinicians, settings and time. The goal of this project was to characterize the information processes involved in nurses' assessment, documentation, decisionmaking and communication regarding patients' mental status in the inpatient setting. VA nurse managers of medical wards (n=18) were systematically selected across the US. A semi-structured telephone interview focused on current assessment, documentation, and communication processes, as well as clinical and administrative decision-making was conducted, audio-recorded and transcribed. A thematic analytic approach was used. Five themes emerged: 1) Fuzzy Concepts, 2) Grey Data, 3) Process Variability 4) Context is Critical and 5) Goal Conflict. This project describes the vague and variable information processes related to delirium and mental status that undermine effective risk, prevention, identification, communication and mitigation of harm.

Information processing capacity in psychopathy: Effects of anomalous attention.

Science.gov (United States)

Hamilton, Rachel K B; Newman, Joseph P

2018-03-01

Hamilton and colleagues (2015) recently proposed that an integrative deficit in psychopathy restricts simultaneous processing, thereby leaving fewer resources available for information encoding, narrowing the scope of attention, and undermining associative processing. The current study evaluated this parallel processing deficit proposal using the Simultaneous-Sequential paradigm. This investigation marks the first a priori test of the Hamilton et al.'s theoretical framework. We predicted that psychopathy would be associated with inferior performance (as indexed by lower accuracy and longer response time) on trials requiring simultaneous processing of visual information relative to trials necessitating sequential processing. Results were consistent with these predictions, supporting the proposal that psychopathy is characterized by a reduced capacity to process multicomponent perceptual information concurrently. We discuss the potential implications of impaired simultaneous processing for the conceptualization of the psychopathic deficit. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Weather Information Processing

Science.gov (United States)

1991-01-01

Science Communications International (SCI), formerly General Science Corporation, has developed several commercial products based upon experience acquired as a NASA Contractor. Among them are METPRO, a meteorological data acquisition and processing system, which has been widely used, RISKPRO, an environmental assessment system, and MAPPRO, a geographic information system. METPRO software is used to collect weather data from satellites, ground-based observation systems and radio weather broadcasts to generate weather maps, enabling potential disaster areas to receive advance warning. GSC's initial work for NASA Goddard Space Flight Center resulted in METPAK, a weather satellite data analysis system. METPAK led to the commercial METPRO system. The company also provides data to other government agencies, U.S. embassies and foreign countries.

Scalable Networked Information Processing Environment (SNIPE)

Energy Technology Data Exchange (ETDEWEB)

Fagg, G.E.; Moore, K. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Computer Science; Dongarra, J.J. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Computer Science]|[Oak Ridge National Lab., TN (United States). Computer Science and Mathematics Div.; Geist, A. [Oak Ridge National Lab., TN (United States). Computer Science and Mathematics Div.

1997-11-01

SNIPE is a metacomputing system that aims to provide a reliable, secure, fault tolerant environment for long term distributed computing applications and data stores across the global Internet. This system combines global naming and replication of both processing and data to support large scale information processing applications leading to better availability and reliability than currently available with typical cluster computing and/or distributed computer environments.

The effects of mild and severe traumatic brain injury on speed of information processing as measured by the computerized tests of information processing (CTIP).

Science.gov (United States)

Tombaugh, Tom N; Rees, Laura; Stormer, Peter; Harrison, Allyson G; Smith, Andra

2007-01-01

In spite of the fact that reaction time (RT) measures are sensitive to the effects of traumatic brain injury (TBI), few RT procedures have been developed for use in standard clinical evaluations. The computerized test of information processing (CTIP) [Tombaugh, T. N., & Rees, L. (2000). Manual for the computerized tests of information processing (CTIP). Ottawa, Ont.: Carleton University] was designed to measure the degree to which TBI decreases the speed at which information is processed. The CTIP consists of three computerized programs that progressively increase the amount of information that is processed. Results of the current study demonstrated that RT increased as the difficulty of the CTIP tests increased (known as the complexity effect), and as severity of injury increased (from mild to severe TBI). The current study also demonstrated the importance of selecting a non-biased measure of variability. Overall, findings suggest that the CTIP is an easy to administer and sensitive measure of information processing speed.

1st International Conference on Cognitive Systems and Information Processing

CERN Document Server

Hu, Dewen; Liu, Huaping

2014-01-01

"Foundations and Practical Applications of Cognitive Systems and Information Processing" presents selected papers from the First International Conference on Cognitive Systems and Information Processing, held in Beijing, China on December 15-17, 2012 (CSIP2012). The aim of this conference is to bring together experts from different fields of expertise to discuss the state-of-the-art in artificial cognitive systems and advanced information processing, and to present new findings and perspectives on future development. This book introduces multidisciplinary perspectives on the subject areas of Cognitive Systems and Information Processing, including cognitive sciences and technology, autonomous vehicles, cognitive psychology, cognitive metrics, information fusion, image/video understanding, brain-computer interfaces, visual cognitive processing, neural computation, bioinformatics, etc. The book will be beneficial for both researchers and practitioners in the fields of Cognitive Science, Computer Science and Cogni...

Working memory capacity and redundant information processing efficiency.

Science.gov (United States)

Endres, Michael J; Houpt, Joseph W; Donkin, Chris; Finn, Peter R

2015-01-01

Working memory capacity (WMC) is typically measured by the amount of task-relevant information an individual can keep in mind while resisting distraction or interference from task-irrelevant information. The current research investigated the extent to which differences in WMC were associated with performance on a novel redundant memory probes (RMP) task that systematically varied the amount of to-be-remembered (targets) and to-be-ignored (distractor) information. The RMP task was designed to both facilitate and inhibit working memory search processes, as evidenced by differences in accuracy, response time, and Linear Ballistic Accumulator (LBA) model estimates of information processing efficiency. Participants (N = 170) completed standard intelligence tests and dual-span WMC tasks, along with the RMP task. As expected, accuracy, response-time, and LBA model results indicated memory search and retrieval processes were facilitated under redundant-target conditions, but also inhibited under mixed target/distractor and redundant-distractor conditions. Repeated measures analyses also indicated that, while individuals classified as high (n = 85) and low (n = 85) WMC did not differ in the magnitude of redundancy effects, groups did differ in the efficiency of memory search and retrieval processes overall. Results suggest that redundant information reliably facilitates and inhibits the efficiency or speed of working memory search, and these effects are independent of more general limits and individual differences in the capacity or space of working memory.

Information processing speed in obstructive sleep apnea syndrome: a review.

Science.gov (United States)

Kilpinen, R; Saunamäki, T; Jehkonen, M

2014-04-01

To provide a comprehensive review of studies on information processing speed in patients with obstructive sleep apnea syndrome (OSAS) as compared to healthy controls and normative data, and to determine whether continuous positive airway pressure (CPAP) treatment improves information processing speed. A systematic review was performed on studies drawn from Medline and PsycINFO (January 1990-December 2011) and identified from lists of references in these studies. After inclusion criteria, 159 articles were left for abstract review, and after exclusion criteria 44 articles were fully reviewed. The number of patients in the studies reviewed ranged from 10 to 157 and the study samples consisted mainly of men. Half of the studies reported that patients with OSAS showed reduced information processing speed when compared to healthy controls. Reduced information processing speed was seen more often (75%) when compared to norm-referenced data. Psychomotor speed seemed to be particularly liable to change. CPAP treatment improved processing speed, but the improvement was marginal when compared to placebo or conservative treatment. Patients with OSAS are affected by reduced information processing speed, which may persist despite CPAP treatment. Information processing is usually assessed as part of other cognitive functioning, not as a cognitive domain per se. However, it is important to take account of information processing speed when assessing other aspects of cognitive functioning. This will make it possible to determine whether cognitive decline in patients with OSAS is based on lower-level or higher-level cognitive processes or both. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Strategic-Decision Quality in Public Organizations: An Information Processing Perspective.

NARCIS (Netherlands)

B.R.J. George (Bert); S. Desmidt (Sebastian)

2016-01-01

textabstractThis study draws on information processing theory to investigate predictors of strategic-decision quality in public organizations. Information processing theory argues that (a) rational planning practices contribute to strategic-decision quality by injecting information into decision

Optimal Information Processing in Biochemical Networks

Science.gov (United States)

Wiggins, Chris

2012-02-01

A variety of experimental results over the past decades provide examples of near-optimal information processing in biological networks, including in biochemical and transcriptional regulatory networks. Computing information-theoretic quantities requires first choosing or computing the joint probability distribution describing multiple nodes in such a network --- for example, representing the probability distribution of finding an integer copy number of each of two interacting reactants or gene products while respecting the `intrinsic' small copy number noise constraining information transmission at the scale of the cell. I'll given an overview of some recent analytic and numerical work facilitating calculation of such joint distributions and the associated information, which in turn makes possible numerical optimization of information flow in models of noisy regulatory and biochemical networks. Illustrating cases include quantification of form-function relations, ideal design of regulatory cascades, and response to oscillatory driving.

FY 2000 report on the results of the R and D of the fusion domain. Volume 3. Biomolecular mechanism and design; 2000 nendo yugo ryoiki kenkyu kaihatsu. 3. Biomolecular mechanism and design

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-03-01

For the purpose of creating cells/tissue assemblies and the molecular machine that substitute for self-organizing and self-repairing functions of a living body outside the body, the basic technology research was conducted, and the FY 2000 results were reported. In the study of 3D cell and tissue module engineering, the following were conducted: study of the surface modification and functional expression of biomaterials, study of the mechanical stress to cartilaginous cells and the response, development of the production method of biodegradable synthetic polymer porous materials, study of organism hard tissue materials/bone remodeling and cultured bone transportation, development of zinc-releasing calcium phosphate ceramics. In the study of biomolecular mechanism and design, 1D unidirectional movement of microtubules by applying microlithography technology, structural study of kinesin-family molecular motor by low temperature microscope, ribozyme and the application to leukemia, basic study on assessment of chemical substances by human cultured cells, study of a low molecule detection system using nucleic acid and peptide. (NEDO)

LanguageNet: A Novel Framework for Processing Unstructured Text Information

DEFF Research Database (Denmark)

Qureshi, Pir Abdul Rasool; Memon, Nasrullah; Wiil, Uffe Kock

2011-01-01

In this paper we present LanguageNet—a novel framework for processing unstructured text information from human generated content. The state of the art information processing frameworks have some shortcomings: modeled in generalized form, trained on fixed (limited) data sets, and leaving...... the specialization necessary for information consolidation to the end users. The proposed framework is the first major attempt to address these shortcomings. LanguageNet provides extended support of graphical methods contributing added value to the capabilities of information processing. We discuss the benefits...... of the framework and compare it with the available state of the art. We also describe how the framework improves the information gathering process and contribute towards building systems with better performance in the domain of Open Source Intelligence....

Environmental Light and Its Relationship with Electromagnetic Resonances of Biomolecular Interactions, as Predicted by the Resonant Recognition Model

Directory of Open Access Journals (Sweden)

Irena Cosic

2016-06-01

Full Text Available The meaning and influence of light to biomolecular interactions, and consequently to health, has been analyzed using the Resonant Recognition Model (RRM. The RRM proposes that biological processes/interactions are based on electromagnetic resonances between interacting biomolecules at specific electromagnetic frequencies within the infra-red, visible and ultra-violet frequency ranges, where each interaction can be identified by the certain frequency critical for resonant activation of specific biological activities of proteins and DNA. We found that: (1 the various biological interactions could be grouped according to their resonant frequency into super families of these functions, enabling simpler analyses of these interactions and consequently analyses of influence of electromagnetic frequencies to health; (2 the RRM spectrum of all analyzed biological functions/interactions is the same as the spectrum of the sun light on the Earth, which is in accordance with fact that life is sustained by the sun light; (3 the water is transparent to RRM frequencies, enabling proteins and DNA to interact without loss of energy; (4 the spectrum of some artificial sources of light, as opposed to the sun light, do not cover the whole RRM spectrum, causing concerns for disturbance to some biological functions and consequently we speculate that it can influence health.

Processing reafferent and exafferent visual information for action and perception.

Science.gov (United States)

Reichenbach, Alexandra; Diedrichsen, Jörn

2015-01-01

A recent study suggests that reafferent hand-related visual information utilizes a privileged, attention-independent processing channel for motor control. This process was termed visuomotor binding to reflect its proposed function: linking visual reafferences to the corresponding motor control centers. Here, we ask whether the advantage of processing reafferent over exafferent visual information is a specific feature of the motor processing stream or whether the improved processing also benefits the perceptual processing stream. Human participants performed a bimanual reaching task in a cluttered visual display, and one of the visual hand cursors could be displaced laterally during the movement. We measured the rapid feedback responses of the motor system as well as matched perceptual judgments of which cursor was displaced. Perceptual judgments were either made by watching the visual scene without moving or made simultaneously to the reaching tasks, such that the perceptual processing stream could also profit from the specialized processing of reafferent information in the latter case. Our results demonstrate that perceptual judgments in the heavily cluttered visual environment were improved when performed based on reafferent information. Even in this case, however, the filtering capability of the perceptual processing stream suffered more from the increasing complexity of the visual scene than the motor processing stream. These findings suggest partly shared and partly segregated processing of reafferent information for vision for motor control versus vision for perception.

Towards the understanding of network information processing in biology

Science.gov (United States)

Singh, Vijay

Living organisms perform incredibly well in detecting a signal present in the environment. This information processing is achieved near optimally and quite reliably, even though the sources of signals are highly variable and complex. The work in the last few decades has given us a fair understanding of how individual signal processing units like neurons and cell receptors process signals, but the principles of collective information processing on biological networks are far from clear. Information processing in biological networks, like the brain, metabolic circuits, cellular-signaling circuits, etc., involves complex interactions among a large number of units (neurons, receptors). The combinatorially large number of states such a system can exist in makes it impossible to study these systems from the first principles, starting from the interactions between the basic units. The principles of collective information processing on such complex networks can be identified using coarse graining approaches. This could provide insights into the organization and function of complex biological networks. Here I study models of biological networks using continuum dynamics, renormalization, maximum likelihood estimation and information theory. Such coarse graining approaches identify features that are essential for certain processes performed by underlying biological networks. We find that long-range connections in the brain allow for global scale feature detection in a signal. These also suppress the noise and remove any gaps present in the signal. Hierarchical organization with long-range connections leads to large-scale connectivity at low synapse numbers. Time delays can be utilized to separate a mixture of signals with temporal scales. Our observations indicate that the rules in multivariate signal processing are quite different from traditional single unit signal processing.

Information technology, knowledge processes, and innovation success

NARCIS (Netherlands)

Song, X.M.; Zang, F.; Bij, van der J.D.; Weggeman, M.C.D.P.

2001-01-01

Despite the obvious linkage between information technologies (IT) and knowledge processes and the apparent strategic importance of both, little research has done to explicitly examine how, if at all, IT and knowledge processes affect firm outcomes. The purpose of this study is to bridge this

Photonic Quantum Information Processing

International Nuclear Information System (INIS)

Walther, P.

2012-01-01

The advantage of the photon's mobility makes optical quantum system ideally suited for delegated quantum computation. I will present results for the realization for a measurement-based quantum network in a client-server environment, where quantum information is securely communicated and computed. Related to measurement-based quantum computing I will discuss a recent experiment showing that quantum discord can be used as resource for the remote state preparation, which might shine new light on the requirements for quantum-enhanced information processing. Finally, I will briefly review recent photonic quantum simulation experiments of four frustrated Heisenberg-interactions spins and present an outlook of feasible simulation experiments with more complex interactions or random walk structures. As outlook I will discuss the current status of new quantum technology for improving the scalability of photonic quantum systems by using superconducting single-photon detectors and tailored light-matter interactions. (author)

Utility-based early modulation of processing distracting stimulus information.

Science.gov (United States)

Wendt, Mike; Luna-Rodriguez, Aquiles; Jacobsen, Thomas

2014-12-10

Humans are selective information processors who efficiently prevent goal-inappropriate stimulus information to gain control over their actions. Nonetheless, stimuli, which are both unnecessary for solving a current task and liable to cue an incorrect response (i.e., "distractors"), frequently modulate task performance, even when consistently paired with a physical feature that makes them easily discernible from target stimuli. Current models of cognitive control assume adjustment of the processing of distractor information based on the overall distractor utility (e.g., predictive value regarding the appropriate response, likelihood to elicit conflict with target processing). Although studies on distractor interference have supported the notion of utility-based processing adjustment, previous evidence is inconclusive regarding the specificity of this adjustment for distractor information and the stage(s) of processing affected. To assess the processing of distractors during sensory-perceptual phases we applied EEG recording in a stimulus identification task, involving successive distractor-target presentation, and manipulated the overall distractor utility. Behavioral measures replicated previously found utility modulations of distractor interference. Crucially, distractor-evoked visual potentials (i.e., posterior N1) were more pronounced in high-utility than low-utility conditions. This effect generalized to distractors unrelated to the utility manipulation, providing evidence for item-unspecific adjustment of early distractor processing to the experienced utility of distractor information. Copyright © 2014 the authors 0270-6474/14/3416720-06$15.00/0.

INFORMATION SYSTEM OF AUTOMATION OF PREPARATION EDUCATIONAL PROCESS DOCUMENTS

Directory of Open Access Journals (Sweden)

V. A. Matyushenko

2016-01-01

Full Text Available Information technology is rapidly conquering the world, permeating all spheres of human activity. Education is not an exception. An important direction of information of education is the development of university management systems. Modern information systems improve and facilitate the management of all types of activities of the institution. The purpose of this paper is development of system, which allows automating process of formation of accounting documents. The article describes the problem of preparation of the educational process documents. Decided to project and create the information system in Microsoft Access environment. The result is four types of reports obtained by using the developed system. The use of this system now allows you to automate the process and reduce the effort required to prepare accounting documents. All reports was implement in Microsoft Excel software product and can be used for further analysis and processing.

Wave-processing of long-scale information by neuronal chains.

Directory of Open Access Journals (Sweden)

José Antonio Villacorta-Atienza

Full Text Available Investigation of mechanisms of information handling in neural assemblies involved in computational and cognitive tasks is a challenging problem. Synergetic cooperation of neurons in time domain, through synchronization of firing of multiple spatially distant neurons, has been widely spread as the main paradigm. Complementary, the brain may also employ information coding and processing in spatial dimension. Then, the result of computation depends also on the spatial distribution of long-scale information. The latter bi-dimensional alternative is notably less explored in the literature. Here, we propose and theoretically illustrate a concept of spatiotemporal representation and processing of long-scale information in laminar neural structures. We argue that relevant information may be hidden in self-sustained traveling waves of neuronal activity and then their nonlinear interaction yields efficient wave-processing of spatiotemporal information. Using as a testbed a chain of FitzHugh-Nagumo neurons, we show that the wave-processing can be achieved by incorporating into the single-neuron dynamics an additional voltage-gated membrane current. This local mechanism provides a chain of such neurons with new emergent network properties. In particular, nonlinear waves as a carrier of long-scale information exhibit a variety of functionally different regimes of interaction: from complete or asymmetric annihilation to transparent crossing. Thus neuronal chains can work as computational units performing different operations over spatiotemporal information. Exploiting complexity resonance these composite units can discard stimuli of too high or too low frequencies, while selectively compress those in the natural frequency range. We also show how neuronal chains can contextually interpret raw wave information. The same stimulus can be processed differently or identically according to the context set by a periodic wave train injected at the opposite end of the

Role of Information Anxiety and Information Load on Processing of Prescription Drug Information Leaflets.

Science.gov (United States)

Bapat, Shweta S; Patel, Harshali K; Sansgiry, Sujit S

2017-10-16

In this study, we evaluate the role of information anxiety and information load on the intention to read information from prescription drug information leaflets (PILs). These PILs were developed based on the principals of information load and consumer information processing. This was an experimental prospective repeated measures study conducted in the United States where 360 (62% response rate) university students (>18 years old) participated. Participants were presented with a scenario followed by exposure to the three drug product information sources used to operationalize information load. The three sources were: (i) current practice; (ii) pre-existing one-page text only; and (iii) interventional one-page prototype PILs designed for the study. Information anxiety was measured as anxiety experienced by the individual when encountering information. The outcome variable of intention to read PILs was defined as the likelihood that the patient will read the information provided in the leaflets. A survey questionnaire was used to capture the data and the objectives were analyzed by performing a repeated measures MANOVA using SAS version 9.3. When compared to current practice and one-page text only leaflets, one-page PILs had significantly lower scores on information anxiety ( p information load ( p Information anxiety and information load significantly impacted intention to read ( p < 0.001). Newly developed PILs increased patient's intention to read and can help in improving the counseling services provided by pharmacists.

IMPROVING THE QUALITY OF MAINTENANCE PROCESSES USING INFORMATION TECHNOLOGY

Directory of Open Access Journals (Sweden)

Zora Arsovski

2008-06-01

Full Text Available In essence, process of maintaining equipment is a support process, because it indirectly contributes to operational ability of the production process necessary for the supply chain of the new value. Taking into account increased levels of automatization and quality, this proces s becomes more and more significant and for some branches of industry, even crucial. Due to the fact that the quality of the entire process is more and more dependent on the maintenance process, these processes must be carefully designed and effectively im plemented. There are various techniques and approaches at our disposal, such as technical, logistical and intensive application of the information - communication technologies. This last approach is presented in this work. It begins with organizational goa ls, especially quality objectives. Then, maintenance processes and integrated information system structures are defined. Maintenance process quality and improvement processes are defined using a set of performances, with a special emphasis placed on effectiveness and quality economics. At the end of the work, information system for improving maintenance economics is structured. Besides theoretical analysis, work also presents results authors obtained analyzing food industry, metal processing industry an d building materials industry.

Markovian Processes for Quantitative Information Leakage

DEFF Research Database (Denmark)

Biondi, Fabrizio

Quantification of information leakage is a successful approach for evaluating the security of a system. It models the system to be analyzed as a channel with the secret as the input and an output as observable by the attacker as the output, and applies information theory to quantify the amount...... and randomized processes with Markovian models and to compute their information leakage for a very general model of attacker. We present the QUAIL tool that automates such analysis and is able to compute the information leakage of an imperative WHILE language. Finally, we show how to use QUAIL to analyze some...... of information transmitted through such channel, thus effectively quantifying how many bits of the secret can be inferred by the attacker by analyzing the system’s output. Channels are usually encoded as matrices of conditional probabilities, known as channel matrices. Such matrices grow exponentially...

Evaluation of EMG processing techniques using Information Theory.

Science.gov (United States)

Farfán, Fernando D; Politti, Julio C; Felice, Carmelo J

2010-11-12

Electromyographic signals can be used in biomedical engineering and/or rehabilitation field, as potential sources of control for prosthetics and orthotics. In such applications, digital processing techniques are necessary to follow efficient and effectively the changes in the physiological characteristics produced by a muscular contraction. In this paper, two methods based on information theory are proposed to evaluate the processing techniques. These methods determine the amount of information that a processing technique is able to extract from EMG signals. The processing techniques evaluated with these methods were: absolute mean value (AMV), RMS values, variance values (VAR) and difference absolute mean value (DAMV). EMG signals from the middle deltoid during abduction and adduction movement of the arm in the scapular plane was registered, for static and dynamic contractions. The optimal window length (segmentation), abduction and adduction movements and inter-electrode distance were also analyzed. Using the optimal segmentation (200 ms and 300 ms in static and dynamic contractions, respectively) the best processing techniques were: RMS, AMV and VAR in static contractions, and only the RMS in dynamic contractions. Using the RMS of EMG signal, variations in the amount of information between the abduction and adduction movements were observed. Although the evaluation methods proposed here were applied to standard processing techniques, these methods can also be considered as alternatives tools to evaluate new processing techniques in different areas of electrophysiology.

49 CFR 564.5 - Information filing; agency processing of filings.

Science.gov (United States)

2010-10-01

... 49 Transportation 6 2010-10-01 2010-10-01 false Information filing; agency processing of filings... HIGHWAY TRAFFIC SAFETY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION REPLACEABLE LIGHT SOURCE INFORMATION (Eff. until 12-01-12) § 564.5 Information filing; agency processing of filings. (a) Each manufacturer...

Affect and Persuasion: Effects on Motivation for Information Processing.

Science.gov (United States)

Leach, Mark M; Stoltenberg, Cal D.

The relationship between mood and information processing, particularly when reviewing the Elaboration Likelihood Model of persuasion, lacks conclusive evidence. This study was designed to investigate the hypothesis that information processing would be greater for mood-topic congruence than non mood-topic congruence. Undergraduate students (N=216)…

Deriving Structural Information from Experimentally Measured Data on Biomolecules.

Science.gov (United States)

van Gunsteren, Wilfred F; Allison, Jane R; Daura, Xavier; Dolenc, Jožica; Hansen, Niels; Mark, Alan E; Oostenbrink, Chris; Rusu, Victor H; Smith, Lorna J

2016-12-23

During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Q exp of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Q exp , 2) inaccuracies in the function Q(r→) used to relate the quantity Q to structure r→ , 3) how to account for the averaging inherent in the measurement of Q exp , 4) how to handle the possible multiple-valuedness of the inverse r→(Q) of the function Q(r→) , to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X-ray and neutron diffraction, small-angle and wide-angle X-ray scattering, free-electron laser imaging, cryo-electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion-mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non-experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Monkeys preferentially process body information while viewing affective displays.

Science.gov (United States)

Bliss-Moreau, Eliza; Moadab, Gilda; Machado, Christopher J

2017-08-01

Despite evolutionary claims about the function of facial behaviors across phylogeny, rarely are those hypotheses tested in a comparative context-that is, by evaluating how nonhuman animals process such behaviors. Further, while increasing evidence indicates that humans make meaning of faces by integrating contextual information, including that from the body, the extent to which nonhuman animals process contextual information during affective displays is unknown. In the present study, we evaluated the extent to which rhesus macaques (Macaca mulatta) process dynamic affective displays of conspecifics that included both facial and body behaviors. Contrary to hypotheses that they would preferentially attend to faces during affective displays, monkeys looked for longest, most frequently, and first at conspecifics' bodies rather than their heads. These findings indicate that macaques, like humans, attend to available contextual information during the processing of affective displays, and that the body may also be providing unique information about affective states. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

[Postdonation information: the French fourth hemovigilance sub-process].

Science.gov (United States)

Py, J-Y; Sandid, I; Jbilou, S; Dupuis, M; Adda, R; Narbey, D; Djoudi, R

2014-11-01

Postdonation information is the knowledge of information about the donor or his donation, occurring after it, which challenges quality or safety of the blood products stemming from this or other donations. Classical hemovigilance sub-processes concerning donors or recipients adverse events do not cover this topic. France is just about to make it official as a fourth sub-process. Less formal management of postdonation information is already set up for more than ten years. French data of the year 2013 are presented, including the regional notification level and the national reporting one. A significant level of heterogeneity is observed as for other hemovigilance sub-processes. It is mainly due to subjective rather than objective differences in risk appreciation. A real consensual work is expected about it in the future. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Real-time information and processing system for radiation protection

International Nuclear Information System (INIS)

Oprea, I.; Oprea, M.; Stoica, M.; Badea, E.; Guta, V.

1999-01-01

The real-time information and processing system has as main task to record, collect, process and transmit the radiation level and weather data, being proposed for radiation protection, environmental monitoring around nuclear facilities and for civil defence. Such a system can offer information in order to provide mapping, data base, modelling and communication and to assess the consequences of nuclear accidents. The system incorporates a number of stationary or mobile radiation monitoring equipment, weather parameter measuring station, a GIS-based information processing center and the communication network, all running on a real-time operating system. It provides the automatic data collection on-line and off-line, remote diagnostic, advanced presentation techniques, including a graphically oriented executive support, which has the ability to respond to an emergency by geographical representation of the hazard zones on the map.The system can be integrated into national or international environmental monitoring systems, being based on local intelligent measuring and transmission units, simultaneous processing and data presentation using a real-time operating system for PC and geographical information system (GIS). Such an integrated system is composed of independent applications operating under the same computer, which is capable to improve the protection of the population and decision makers efforts, updating the remote GIS data base. All information can be managed directly from the map by multilevel data retrieving and presentation by using on-line dynamic evolution of the events, environment information, evacuation optimization, image and voice processing

Biomolecular detection using a metal semiconductor field effect transistor

Science.gov (United States)

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

2010-04-01

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

A Study on Improving Information Processing Abilities Based on PBL

Science.gov (United States)

Kim, Du Gyu; Lee, JaeMu

2014-01-01

This study examined an instruction method for the improvement of information processing abilities in elementary school students. Current elementary students are required to develop information processing abilities to create new knowledge for this digital age. There is, however, a shortage of instruction strategies for these information processing…

A Conceptual Model of the Cognitive Processing of Environmental Distance Information

Science.gov (United States)

Montello, Daniel R.

I review theories and research on the cognitive processing of environmental distance information by humans, particularly that acquired via direct experience in the environment. The cognitive processes I consider for acquiring and thinking about environmental distance information include working-memory, nonmediated, hybrid, and simple-retrieval processes. Based on my review of the research literature, and additional considerations about the sources of distance information and the situations in which it is used, I propose an integrative conceptual model to explain the cognitive processing of distance information that takes account of the plurality of possible processes and information sources, and describes conditions under which particular processes and sources are likely to operate. The mechanism of summing vista distances is identified as widely important in situations with good visual access to the environment. Heuristics based on time, effort, or other information are likely to play their most important role when sensory access is restricted.

Information processing. [in human performance

Science.gov (United States)

Wickens, Christopher D.; Flach, John M.

1988-01-01

Theoretical models of sensory-information processing by the human brain are reviewed from a human-factors perspective, with a focus on their implications for aircraft and avionics design. The topics addressed include perception (signal detection and selection), linguistic factors in perception (context provision, logical reversals, absence of cues, and order reversals), mental models, and working and long-term memory. Particular attention is given to decision-making problems such as situation assessment, decision formulation, decision quality, selection of action, the speed-accuracy tradeoff, stimulus-response compatibility, stimulus sequencing, dual-task performance, task difficulty and structure, and factors affecting multiple task performance (processing modalities, codes, and stages).

AGING, CAFFEINE, AND INFORMATION-PROCESSING - AN EVENT-RELATED POTENTIAL ANALYSIS

NARCIS (Netherlands)

LORIST, MM; SNEL, J; MULDER, G; KOK, A

Structural and energetic processes in information processing were studied in young and elderly subjects. A visually focussed selective search task was used, in which subjects had to select relevant information, followed by controlled memory search processes to locate a target item. Caffeine was used

A Reaction Database for Small Molecule Pharmaceutical Processes Integrated with Process Information

DEFF Research Database (Denmark)

Papadakis, Emmanouil; Anantpinijwatna, Amata; Woodley, John

2017-01-01

This article describes the development of a reaction database with the objective to collect data for multiphase reactions involved in small molecule pharmaceutical processes with a search engine to retrieve necessary data in investigations of reaction-separation schemes, such as the role of organic......; compounds participating in the reaction; use of organic solvents and their function; information for single step and multistep reactions; target products; reaction conditions and reaction data. Information for reactor scale-up together with information for the separation and other relevant information...

Teaching Information Systems Development via Process Variants

Science.gov (United States)

Tan, Wee-Kek; Tan, Chuan-Hoo

2010-01-01

Acquiring the knowledge to assemble an integrated Information System (IS) development process that is tailored to the specific needs of a project has become increasingly important. It is therefore necessary for educators to impart to students this crucial skill. However, Situational Method Engineering (SME) is an inherently complex process that…

A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus-response experimental data.

Science.gov (United States)

Cho, Kwang-Hyun; Choo, Sang-Mok; Wellstead, Peter; Wolkenhauer, Olaf

2005-08-15

We propose a unified framework for the identification of functional interaction structures of biomolecular networks in a way that leads to a new experimental design procedure. In developing our approach, we have built upon previous work. Thus we begin by pointing out some of the restrictions associated with existing structure identification methods and point out how these restrictions may be eased. In particular, existing methods use specific forms of experimental algebraic equations with which to identify the functional interaction structure of a biomolecular network. In our work, we employ an extended form of these experimental algebraic equations which, while retaining their merits, also overcome some of their disadvantages. Experimental data are required in order to estimate the coefficients of the experimental algebraic equation set associated with the structure identification task. However, experimentalists are rarely provided with guidance on which parameters to perturb, and to what extent, to perturb them. When a model of network dynamics is required then there is also the vexed question of sample rate and sample time selection to be resolved. Supplying some answers to these questions is the main motivation of this paper. The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841-12846) and Sontag et al. (Bioinformatics 20 (2004) 1877-1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.

Quantum information processing with atoms and photons

International Nuclear Information System (INIS)

Monroe, C.

2003-01-01

Quantum information processors exploit the quantum features of superposition and entanglement for applications not possible in classical devices, offering the potential for significant improvements in the communication and processing of information. Experimental realization of large-scale quantum information processors remains a long term vision, as the required nearly pure quantum behaviour is observed only in exotic hardware such as individual laser-cooled atoms and isolated photons. But recent theoretical and experimental advances suggest that cold atoms and individual photons may lead the way towards bigger and better quantum information processors, effectively building mesoscopic versions of Schroedinger's cat' from the bottom up. (author)

Physics Colloquium: The optical route to quantum information processing

CERN Multimedia

Université de Genève

2011-01-01

Geneva University Physics Department 24, Quai Ernest Ansermet CH-1211 Geneva 4 Monday 11 April 2011 17h00 - Ecole de Physique, Auditoire Stückelberg The optical route to quantum information processing Prof. Terry Rudolph/Imperial College, London Photons are attractive as carriers of quantum information both because they travel, and can thus transmit information, but also because of their good coherence properties and ease in undergoing single-qubit manipulations. The main obstacle to their use in information processing is inducing an effective interaction between them in order to produce entanglement. The most promising approach in photon-based information processing architectures is so-called measurement-based quantum computing. This relies on creating upfront a multi-qubit highly entangled state (the cluster state) which has the remarkable property that, once prepared, it can be used to perform quantum computation by making only single qubit measurements. In this talk I will discuss generically the...

Virtual HRD and National Culture: An Information Processing Perspective

Science.gov (United States)

Chung, Chih-Hung; Angnakoon, Putthachat; Li, Jessica; Allen, Jeff

2016-01-01

Purpose: The purpose of this study is to provide researchers with a better understanding of the cultural impact on information processing in virtual learning environment. Design/methodology/approach: This study uses a causal loop diagram to depict the cultural impact on information processing in the virtual human resource development (VHRD)…

Strategic-decision quality in public organizations : an information processing perspective

OpenAIRE

George, Bert; Desmidt, Sebastian

2018-01-01

textabstractThis study draws on information processing theory to investigate predictors of strategic-decision quality in public organizations. Information processing theory argues that (a) rational planning practices contribute to strategic-decision quality by injecting information into decision making and (b) decision makers contribute to strategic-decision quality by exchanging information during decision making. These assumptions are tested upon 55 Flemish pupil guidance centers. Rational ...

A Reaction Database for Small Molecule Pharmaceutical Processes Integrated with Process Information

Directory of Open Access Journals (Sweden)

Emmanouil Papadakis

2017-10-01

Full Text Available This article describes the development of a reaction database with the objective to collect data for multiphase reactions involved in small molecule pharmaceutical processes with a search engine to retrieve necessary data in investigations of reaction-separation schemes, such as the role of organic solvents in reaction performance improvement. The focus of this reaction database is to provide a data rich environment with process information available to assist during the early stage synthesis of pharmaceutical products. The database is structured in terms of reaction classification of reaction types; compounds participating in the reaction; use of organic solvents and their function; information for single step and multistep reactions; target products; reaction conditions and reaction data. Information for reactor scale-up together with information for the separation and other relevant information for each reaction and reference are also available in the database. Additionally, the retrieved information obtained from the database can be evaluated in terms of sustainability using well-known “green” metrics published in the scientific literature. The application of the database is illustrated through the synthesis of ibuprofen, for which data on different reaction pathways have been retrieved from the database and compared using “green” chemistry metrics.

Disjunctive Information Flow for Communicating Processes

DEFF Research Database (Denmark)

Li, Ximeng; Nielson, Flemming; Nielson, Hanne Riis

2016-01-01

The security validation of practical computer systems calls for the ability to specify and verify information flow policies that are dependent on data content. Such policies play an important role in concurrent, communicating systems: consider a scenario where messages are sent to different...... processes according to their tagging. We devise a security type system that enforces content-dependent information flow policies in the presence of communication and concurrency. The type system soundly guarantees a compositional noninterference property. All theoretical results have been formally proved...

Gathering Information from Transport Systems for Processing in Supply Chains

Science.gov (United States)

Kodym, Oldřich; Unucka, Jakub

2016-12-01

Paper deals with complex system for processing information from means of transport acting as parts of train (rail or road). It focuses on automated information gathering using AutoID technology, information transmission via Internet of Things networks and information usage in information systems of logistic firms for support of selected processes on MES and ERP levels. Different kinds of gathered information from whole transport chain are discussed. Compliance with existing standards is mentioned. Security of information in full life cycle is integral part of presented system. Design of fully equipped system based on synthesized functional nodes is presented.

Springfield Processing Plant (SPP) Facility Information

Energy Technology Data Exchange (ETDEWEB)

Leach, Janice; Torres, Teresa M.

2012-10-01

The Springfield Processing Plant is a hypothetical facility. It has been constructed for use in training workshops. Information is provided about the facility and its surroundings, particularly security-related aspects such as target identification, threat data, entry control, and response force data.

Usage of information safety requirements in improving tube bending process

Science.gov (United States)

Livshitz, I. I.; Kunakov, E.; Lontsikh, P. A.

2018-05-01

This article is devoted to an improvement of the technological process's analysis with the information security requirements implementation. The aim of this research is the competition increase analysis in aircraft industry enterprises due to the information technology implementation by the example of the tube bending technological process. The article analyzes tube bending kinds and current technique. In addition, a potential risks analysis in a tube bending technological process is carried out in terms of information security.

Evaluation of EMG processing techniques using Information Theory

Directory of Open Access Journals (Sweden)

Felice Carmelo J

2010-11-01

Full Text Available Abstract Background Electromyographic signals can be used in biomedical engineering and/or rehabilitation field, as potential sources of control for prosthetics and orthotics. In such applications, digital processing techniques are necessary to follow efficient and effectively the changes in the physiological characteristics produced by a muscular contraction. In this paper, two methods based on information theory are proposed to evaluate the processing techniques. Methods These methods determine the amount of information that a processing technique is able to extract from EMG signals. The processing techniques evaluated with these methods were: absolute mean value (AMV, RMS values, variance values (VAR and difference absolute mean value (DAMV. EMG signals from the middle deltoid during abduction and adduction movement of the arm in the scapular plane was registered, for static and dynamic contractions. The optimal window length (segmentation, abduction and adduction movements and inter-electrode distance were also analyzed. Results Using the optimal segmentation (200 ms and 300 ms in static and dynamic contractions, respectively the best processing techniques were: RMS, AMV and VAR in static contractions, and only the RMS in dynamic contractions. Using the RMS of EMG signal, variations in the amount of information between the abduction and adduction movements were observed. Conclusions Although the evaluation methods proposed here were applied to standard processing techniques, these methods can also be considered as alternatives tools to evaluate new processing techniques in different areas of electrophysiology.

Conditioning from an information processing perspective.

Science.gov (United States)

Gallistel, C R.

2003-04-28

The framework provided by Claude Shannon's [Bell Syst. Technol. J. 27 (1948) 623] theory of information leads to a quantitatively oriented reconceptualization of the processes that mediate conditioning. The focus shifts from processes set in motion by individual events to processes sensitive to the information carried by the flow of events. The conception of what properties of the conditioned and unconditioned stimuli are important shifts from the tangible properties to the intangible properties of number, duration, frequency and contingency. In this view, a stimulus becomes a CS if its onset substantially reduces the subject's uncertainty about the time of occurrence of the next US. One way to represent the subject's knowledge of that time of occurrence is by the cumulative probability function, which has two limiting forms: (1) The state of maximal uncertainty (minimal knowledge) is represented by the inverse exponential function for the random rate condition, in which the US is equally likely at any moment. (2) The limit to the subject's attainable certainty is represented by the cumulative normal function, whose momentary expectation is the CS-US latency minus the time elapsed since CS onset. Its standard deviation is the Weber fraction times the CS-US latency.

Biomolecular strategies for cell surface engineering

Science.gov (United States)

Wilson, John Tanner

Islet transplantation has emerged as a promising cell-based therapy for the treatment of diabetes, but its clinical efficacy remains limited by deleterious host responses that underlie islet destruction. In this dissertation, we describe the assembly of ultrathin conformal coatings that confer molecular-level control over the composition and biophysicochemical properties of the islet surface with implications for improving islet engraftment. Significantly, this work provides novel biomolecular strategies for cell surface engineering with broad biomedical and biotechnological applications in cell-based therapeutics and beyond. Encapsulation of cells and tissue offers a rational approach for attenuating deleterious host responses towards transplanted cells, but a need exists to develop cell encapsulation strategies that minimize transplant volume. Towards this end, we endeavored to generate nanothin films of diverse architecture with tunable properties on the extracellular surface of individual pancreatic islets through a process of layer-by-layer (LbL) self assembly. We first describe the formation of poly(ethylene glycol) (PEG)-rich conformal coatings on islets via LbL self assembly of poly(L-lysine)-g-PEG(biotin) and streptavidin. Multilayer thin films conformed to the geometrically and chemically heterogeneous islet surface, and could be assembled without loss of islet viability or function. Significantly, coated islets performed comparably to untreated controls in a murine model of allogenic intraportal islet transplantation, and, to our knowledge, this is the first study to report in vivo survival and function of nanoencapsulated cells or cell aggregates. Based on these findings, we next postulated that structurally similar PLL-g-PEG copolymers comprised of shorter PEG grafts might be used to initiate and propagate the assembly of polyelectrolyte multilayer (PEM) films on pancreatic islets, while simultaneously preserving islet viability. Through control of PLL

Influence Processes for Information Technology Acceptance

DEFF Research Database (Denmark)

Bhattacherjee, Anol; Sanford, Clive Carlton

2006-01-01

This study examines how processes of external influence shape information technology acceptance among potential users, how such influence effects vary across a user population, and whether these effects are persistent over time. Drawing on the elaboration-likelihood model (ELM), we compared two...... alternative influence processes, the central and peripheral routes, in motivating IT acceptance. These processes were respectively operationalized using the argument quality and source credibility constructs, and linked to perceived usefulness and attitude, the core perceptual drivers of IT acceptance. We...... further examined how these influence processes were moderated by users' IT expertise and perceived job relevance and the temporal stability of such influence effects. Nine hypotheses thus developed were empirically validated using a field survey of document management system acceptance at an eastern...

Organizational restructuring in response to changes in information-processing technology

OpenAIRE

Andrzej Baniak; Jacek Cukrowski

1999-01-01

This paper examines the effects of changes in information-processing technology on the efficient organizational forms of data-processing in decision-making systems. Data-processing is modelled in the framework of the dynamic parallel processing model of associative computation with an endogenous set-up costs of the processors. In such a model, the conditions for efficient organization of information-processing are defined and the architecture of the efficient structures is considered. It is s...

Influence of information on behavioral effects in decision processes

OpenAIRE

Angelarosa Longo; Viviana Ventre

2015-01-01

Rational models in decision processes are marked out by many anomalies, caused by behavioral issues. We point out the importance of information in causing inconsistent preferences in a decision process. In a single or multi agent decision process each mental model is influenced by the presence, the absence or false information about the problem or about other members of the decision making group. The difficulty in modeling these effects increases because behavioral biases influence also the m...

Integration of Individual Processes and Information Demand Patterns: A Conceptual Analysis

Directory of Open Access Journals (Sweden)

Michael Leyer

2017-12-01

Full Text Available Individuals need a variety of information when performing their personal processes. However, companies typically know little about the underlying individual demand patterns in these processes. Conceptualizing information demand patterns of individuals is expected to allow for using these as foundation to extend the traditional internal information logistic perspective of companies. Digital options could then be used to align individual and organizational information leading not only to new product and service offers, but also to new work structures in organizations. Thus, we extend prior literature regarding business process management and information logistics by highlighting how information demand patterns (IDP have to be adapted to individual processes. Our exploratory approach is to demonstrate conceptually the conditions and implications of individual IDPs.

Information processing and dynamics in minimally cognitive agents.

Science.gov (United States)

Beer, Randall D; Williams, Paul L

2015-01-01

There has been considerable debate in the literature about the relative merits of information processing versus dynamical approaches to understanding cognitive processes. In this article, we explore the relationship between these two styles of explanation using a model agent evolved to solve a relational categorization task. Specifically, we separately analyze the operation of this agent using the mathematical tools of information theory and dynamical systems theory. Information-theoretic analysis reveals how task-relevant information flows through the system to be combined into a categorization decision. Dynamical analysis reveals the key geometrical and temporal interrelationships underlying the categorization decision. Finally, we propose a framework for directly relating these two different styles of explanation and discuss the possible implications of our analysis for some of the ongoing debates in cognitive science. Copyright © 2014 Cognitive Science Society, Inc.

Development and Validation of the Social Information Processing Application: A Web-Based Measure of Social Information Processing Patterns in Elementary School-Age Boys

Science.gov (United States)

Kupersmidt, Janis B.; Stelter, Rebecca; Dodge, Kenneth A.

2011-01-01

The purpose of this study was to evaluate the psychometric properties of an audio computer-assisted self-interviewing Web-based software application called the Social Information Processing Application (SIP-AP) that was designed to assess social information processing skills in boys in RD through 5th grades. This study included a racially and…

Information Integration; The process of integration, evolution and versioning

NARCIS (Netherlands)

de Keijzer, Ander; van Keulen, Maurice

2005-01-01

At present, many information sources are available wherever you are. Most of the time, the information needed is spread across several of those information sources. Gathering this information is a tedious and time consuming job. Automating this process would assist the user in its task. Integration

Information processing of earth resources data

Science.gov (United States)

Zobrist, A. L.; Bryant, N. A.

1982-01-01

Current trends in the use of remotely sensed data include integration of multiple data sources of various formats and use of complex models. These trends have placed a strain on information processing systems because an enormous number of capabilities are needed to perform a single application. A solution to this problem is to create a general set of capabilities which can perform a wide variety of applications. General capabilities for the Image-Based Information System (IBIS) are outlined in this report. They are then cross-referenced for a set of applications performed at JPL.

The eyes have it: Using eye tracking to inform information processing strategies in multi-attributes choices.

Science.gov (United States)

Ryan, Mandy; Krucien, Nicolas; Hermens, Frouke

2018-04-01

Although choice experiments (CEs) are widely applied in economics to study choice behaviour, understanding of how individuals process attribute information remains limited. We show how eye-tracking methods can provide insight into how decisions are made. Participants completed a CE, while their eye movements were recorded. Results show that although the information presented guided participants' decisions, there were also several processing biases at work. Evidence was found of (a) top-to-bottom, (b) left-to-right, and (c) first-to-last order biases. Experimental factors-whether attributes are defined as "best" or "worst," choice task complexity, and attribute ordering-also influence information processing. How individuals visually process attribute information was shown to be related to their choices. Implications for the design and analysis of CEs and future research are discussed. Copyright © 2017 John Wiley & Sons, Ltd.

Influence of information on behavioral effects in decision processes

Directory of Open Access Journals (Sweden)

Angelarosa Longo

2015-07-01

Full Text Available Rational models in decision processes are marked out by many anomalies, caused by behavioral issues. We point out the importance of information in causing inconsistent preferences in a decision process. In a single or multi agent decision process each mental model is influenced by the presence, the absence or false information about the problem or about other members of the decision making group. The difficulty in modeling these effects increases because behavioral biases influence also the modeler. Behavioral Operational Research (BOR studies these influences to create efficient models to define choices in similar decision processes.

Designing quantum information processing via structural physical approximation.

Science.gov (United States)

Bae, Joonwoo

2017-10-01

In quantum information processing it may be possible to have efficient computation and secure communication beyond the limitations of classical systems. In a fundamental point of view, however, evolution of quantum systems by the laws of quantum mechanics is more restrictive than classical systems, identified to a specific form of dynamics, that is, unitary transformations and, consequently, positive and completely positive maps to subsystems. This also characterizes classes of disallowed transformations on quantum systems, among which positive but not completely maps are of particular interest as they characterize entangled states, a general resource in quantum information processing. Structural physical approximation offers a systematic way of approximating those non-physical maps, positive but not completely positive maps, with quantum channels. Since it has been proposed as a method of detecting entangled states, it has stimulated fundamental problems on classifications of positive maps and the structure of Hermitian operators and quantum states, as well as on quantum measurement such as quantum design in quantum information theory. It has developed efficient and feasible methods of directly detecting entangled states in practice, for which proof-of-principle experimental demonstrations have also been performed with photonic qubit states. Here, we present a comprehensive review on quantum information processing with structural physical approximations and the related progress. The review mainly focuses on properties of structural physical approximations and their applications toward practical information applications.

Regulation of health information processing in an outsourcing environment.

Science.gov (United States)

2004-06-01

Policy makers must consider the work force, technology, cost, and legal implications of their legislative proposals. AHIMA, AAMT, CHIA, and MTIA urge lawmakers to craft regulatory solutions that enforce HIPAA and support advancements in modern health information processing practices that improve the quality and cost of healthcare. We also urge increased investment in health information work force development and implementation of new technologies to advance critical healthcare outcomes--timely, accurate, accessible, and secure information to support patient care. It is essential that state legislatures reinforce the importance of improving information processing solutions for healthcare and not take actions that will produce unintended and detrimental consequences.

Classification of Modern and Old Río Tinto Sedimentary Deposits Through the Biomolecular Record Using a Life Marker Biochip: Implications for Detecting Life on Mars

Science.gov (United States)

Parro, Victor; Fernández-Remolar, David; Rodríguez-Manfredi, José A.; Cruz-Gil, Patricia; Rivas, Luis A.; Ruiz-Bermejo, Marta; Moreno-Paz, Mercedes; García-Villadangos, Miriam; Gómez-Ortiz, David; Blanco-López, Yolanda; Menor-Salván, César; Prieto-Ballesteros, Olga; Gómez-Elvira, Javier

2011-01-01

The particular mineralogy formed in the acidic conditions of the Río Tinto has proven to be a first-order analogue for the acid-sulfate aqueous environments of Mars. Therefore, studies about the formation and preservation of biosignatures in the Río Tinto will provide insights into equivalent processes on Mars. We characterized the biomolecular patterns recorded in samples of modern and old fluvial sediments along a segment of the river by means of an antibody microarray containing more than 200 antibodies (LDCHIP200, for Life Detector Chip) against whole microorganisms, universal biomolecules, or environmental extracts. Samples containing 0.3-0.5g of solid material were automatically analyzed in situ by the Signs Of LIfe Detector instrument (SOLID2), and the results were corroborated by extensive analysis in the laboratory. Positive antigen-antibody reactions indicated the presence of microbial strains or high-molecular-weight biopolymers that originated from them. The LDCHIP200 results were quantified and subjected to a multivariate analysis for immunoprofiling. We associated similar immunopatterns, and biomolecular markers, to samples with similar sedimentary age. Phyllosilicate-rich samples from modern fluvial sediments gave strong positive reactions with antibodies against bacteria of the genus Acidithiobacillus and against biochemical extracts from Río Tinto sediments and biofilms. These samples contained high amounts of sugars (mostly polysaccharides) with monosaccharides like glucose, rhamnose, fucose, and so on. By contrast, the older deposits, which are a mix of clastic sands and evaporites, showed only a few positives with LDCHIP200, consistent with lower protein and sugar content. We conclude that LDCHIP200 results can establish a correlation between microenvironments, diagenetic stages, and age with the biomarker profile associated with a sample. Our results would help in the search for putative martian biomarkers in acidic deposits with similar

Classification of modern and old Río Tinto sedimentary deposits through the biomolecular record using a life marker biochip: implications for detecting life on Mars.

Science.gov (United States)

Parro, Victor; Fernández-Remolar, David; Rodríguez-Manfredi, José A; Cruz-Gil, Patricia; Rivas, Luis A; Ruiz-Bermejo, Marta; Moreno-Paz, Mercedes; García-Villadangos, Miriam; Gómez-Ortiz, David; Blanco-López, Yolanda; Menor-Salván, César; Prieto-Ballesteros, Olga; Gómez-Elvira, Javier

2011-01-01

The particular mineralogy formed in the acidic conditions of the Río Tinto has proven to be a first-order analogue for the acid-sulfate aqueous environments of Mars. Therefore, studies about the formation and preservation of biosignatures in the Río Tinto will provide insights into equivalent processes on Mars. We characterized the biomolecular patterns recorded in samples of modern and old fluvial sediments along a segment of the river by means of an antibody microarray containing more than 200 antibodies (LDCHIP200, for Life Detector Chip) against whole microorganisms, universal biomolecules, or environmental extracts. Samples containing 0.3-0.5 g of solid material were automatically analyzed in situ by the Signs Of LIfe Detector instrument (SOLID2), and the results were corroborated by extensive analysis in the laboratory. Positive antigen-antibody reactions indicated the presence of microbial strains or high-molecular-weight biopolymers that originated from them. The LDCHIP200 results were quantified and subjected to a multivariate analysis for immunoprofiling. We associated similar immunopatterns, and biomolecular markers, to samples with similar sedimentary age. Phyllosilicate-rich samples from modern fluvial sediments gave strong positive reactions with antibodies against bacteria of the genus Acidithiobacillus and against biochemical extracts from Río Tinto sediments and biofilms. These samples contained high amounts of sugars (mostly polysaccharides) with monosaccharides like glucose, rhamnose, fucose, and so on. By contrast, the older deposits, which are a mix of clastic sands and evaporites, showed only a few positives with LDCHIP200, consistent with lower protein and sugar content. We conclude that LDCHIP200 results can establish a correlation between microenvironments, diagenetic stages, and age with the biomarker profile associated with a sample. Our results would help in the search for putative martian biomarkers in acidic deposits with similar

Development of technical information processing system(VI)

Energy Technology Data Exchange (ETDEWEB)

Lee, Jee Hoh; Kim, Tae Hwan; Choi, Kwang; Chung, Hyun Sook; Keum, Jong Yong [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

1994-12-01

This project is to establish high-quality information circulation system by developing serials-control system to improve serials management from ordering to distributing and availability on R and D and to advance in quality of information service needed in R and D by fast retrieval and providing of research information with CD-Net. The results of the project are as follows. 1. Serials management process which covers from ordering to distributing have higher efficiency by development of subscription information system. 2. Systematic control on each issue of serials is achieved by development of serials checking system. 3. It is possible to provide vol. and no. information of issue received currently to researchers promptly by improvement of serials holding information system. 4. Retrieval of research information contained in various CD-ROM DB throughout KAERI-NET is possible by research on construction methods of CD-Net. 2 figs, 25 refs. (Author).

Development of technical information processing system(VI)

International Nuclear Information System (INIS)

Lee, Jee Hoh; Kim, Tae Hwan; Choi, Kwang; Chung, Hyun Sook; Keum, Jong Yong

1994-12-01

This project is to establish high-quality information circulation system by developing serials-control system to improve serials management from ordering to distributing and availability on R and D and to advance in quality of information service needed in R and D by fast retrieval and providing of research information with CD-Net. The results of the project are as follows. 1. Serials management process which covers from ordering to distributing have higher efficiency by development of subscription information system. 2. Systematic control on each issue of serials is achieved by development of serials checking system. 3. It is possible to provide vol. and no. information of issue received currently to researchers promptly by improvement of serials holding information system. 4. Retrieval of research information contained in various CD-ROM DB throughout KAERI-NET is possible by research on construction methods of CD-Net. 2 figs, 25 refs. (Author)

Sources of Information as Determinants of Product and Process Innovation.

Science.gov (United States)

Gómez, Jaime; Salazar, Idana; Vargas, Pilar

2016-01-01

In this paper we use a panel of manufacturing firms in Spain to examine the extent to which they use internal and external sources of information (customers, suppliers, competitors, consultants and universities) to generate product and process innovation. Our results show that, although internal sources are influential, external sources of information are key to achieve innovation performance. These results are in line with the open innovation literature because they show that firms that are opening up their innovation process and that use different information sources have a greater capacity to generate innovations. We also find that the importance of external sources of information varies depending on the type of innovation (product or process) considered. To generate process innovation, firms mainly rely on suppliers while, to generate product innovation, the main contribution is from customers. The potential simultaneity between product and process innovation is also taken into consideration. We find that the generation of both types of innovation is not independent.

Sources of Information as Determinants of Product and Process Innovation.

Directory of Open Access Journals (Sweden)

Jaime Gómez

Full Text Available In this paper we use a panel of manufacturing firms in Spain to examine the extent to which they use internal and external sources of information (customers, suppliers, competitors, consultants and universities to generate product and process innovation. Our results show that, although internal sources are influential, external sources of information are key to achieve innovation performance. These results are in line with the open innovation literature because they show that firms that are opening up their innovation process and that use different information sources have a greater capacity to generate innovations. We also find that the importance of external sources of information varies depending on the type of innovation (product or process considered. To generate process innovation, firms mainly rely on suppliers while, to generate product innovation, the main contribution is from customers. The potential simultaneity between product and process innovation is also taken into consideration. We find that the generation of both types of innovation is not independent.

Sources of Information as Determinants of Product and Process Innovation

Science.gov (United States)

2016-01-01

In this paper we use a panel of manufacturing firms in Spain to examine the extent to which they use internal and external sources of information (customers, suppliers, competitors, consultants and universities) to generate product and process innovation. Our results show that, although internal sources are influential, external sources of information are key to achieve innovation performance. These results are in line with the open innovation literature because they show that firms that are opening up their innovation process and that use different information sources have a greater capacity to generate innovations. We also find that the importance of external sources of information varies depending on the type of innovation (product or process) considered. To generate process innovation, firms mainly rely on suppliers while, to generate product innovation, the main contribution is from customers. The potential simultaneity between product and process innovation is also taken into consideration. We find that the generation of both types of innovation is not independent. PMID:27035456

Distributed quantum information processing via quantum dot spins

International Nuclear Information System (INIS)

Jun, Liu; Qiong, Wang; Le-Man, Kuang; Hao-Sheng, Zeng

2010-01-01

We propose a scheme to engineer a non-local two-qubit phase gate between two remote quantum-dot spins. Along with one-qubit local operations, one can in principal perform various types of distributed quantum information processing. The scheme employs a photon with linearly polarisation interacting one after the other with two remote quantum-dot spins in cavities. Due to the optical spin selection rule, the photon obtains a Faraday rotation after the interaction process. By measuring the polarisation of the final output photon, a non-local two-qubit phase gate between the two remote quantum-dot spins is constituted. Our scheme may has very important applications in the distributed quantum information processing

Modeling biochemical transformation processes and information processing with Narrator.

Science.gov (United States)

Mandel, Johannes J; Fuss, Hendrik; Palfreyman, Niall M; Dubitzky, Werner

2007-03-27

Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Narrator is a flexible and intuitive systems biology tool. It is

Life-cycle support for staff assignment rules in process-aware information systems

NARCIS (Netherlands)

Rinderle-Ma, S.; Aalst, van der W.M.P.

2007-01-01

Process mining has been proposed as a tool for analyzing business processes based on events logs. Today, most information systems are logging events in some log and thus provide detailed information about the processes they are supporting. This information can be used for two forms of process

Evaluating nurse understanding and participation in the informed consent process.

Science.gov (United States)

Axson, Sydney A; Giordano, Nicholas A; Hermann, Robin M; Ulrich, Connie M

2017-01-01

Informed consent is fundamental to the autonomous decision-making of patients, yet much is still unknown about the process in the clinical setting. In an evolving healthcare landscape, nurses must be prepared to address patient understanding and participate in the informed consent process to better fulfill their well-established role as patient advocates. This study examines hospital-based nurses' experiences and understandings of the informed consent process. This qualitative descriptive study utilized a semi-structured interview approach identifying thematic concerns, experiences, and knowledge of informed consent across a selected population of clinically practicing nurses. Participants and research context: In all, 20 baccalaureate prepared registered nurses practicing in various clinical settings (i.e. critical care, oncology, medical/surgical) at a large northeastern academic medical center in the United States completed semi-structured interviews and a demographic survey. The mean age of participants was 36.6 years old, with a mean of 12.2 years of clinical experience. Ethical considerations: Participation in this study involved minimal risk and no invasive measures. This study received Institutional Review Board approval from the University of Pennsylvania. All participants voluntarily consented. The majority of participants (N = 19) believe patient safety is directly linked to patient comprehension of the informed consent process. However, when asked if nurses have a defined role in the informed consent process, nearly half did not agree (N = 9). Through this qualitative approach, three major nursing roles emerged: the nurse as a communicator, the nurse as an advocate, and the clerical role of the nurse. This investigation contributes to the foundation of ethical research that will better prepare nurses for patient engagement, advance current understanding of informed consent, and allow for future development of solutions. Nurses are at the forefront of

Application of information and communication technology in process reengineering

Directory of Open Access Journals (Sweden)

Đurović Aleksandar M.

2014-01-01

Full Text Available This paper examines the role of information communication technologies in reengineering processes. General analysis of a process will show that information communication technologies improve their efficiency. Reengineering model based on the BPMN 2.0 standard will be applied to the process of seeking internship/job by students from Faculty of Transport and Traffic Engineering. In the paper, after defining the technical characteristics and required functionalities, web / mobile application is proposed, enabling better visibility of traffic engineers to companies seeking that education profile.

Information Processing Bias in Post-traumatic Stress Disorder

OpenAIRE

Weber, Darren L

2008-01-01

This review considers theory and evidence for abnormal information processing in post-traumatic stress disorder (PTSD). Cognitive studies have indicated sensitivity in PTSD for traumatic information, more so than general emotional information. These findings were supported by neuroimaging studies that identify increased brain activity during traumatic cognition, especially in affective networks (including the amygdala, orbitofrontal and anterior cingulate cortex). In theory, it is proposed th...

Towards Web-based representation and processing of health information

DEFF Research Database (Denmark)

Gao, S.; Mioc, Darka; Yi, X.L.

2009-01-01

facilitated the online processing, mapping and sharing of health information, with the use of HERXML and Open Geospatial Consortium (OGC) services. It brought a new solution in better health data representation and initial exploration of the Web-based processing of health information. Conclusion: The designed......Background: There is great concern within health surveillance, on how to grapple with environmental degradation, rapid urbanization, population mobility and growth. The Internet has emerged as an efficient way to share health information, enabling users to access and understand data....... For the representation of health information through Web-mapping applications, there still lacks a standard format to accommodate all fixed (such as location) and variable (such as age, gender, health outcome, etc) indicators in the representation of health information. Furthermore, net-centric computing has not been...

Team confidence, motivated information processing, and dynamic group decision making

NARCIS (Netherlands)

de Dreu, C.K.W.; Beersma, B.

2010-01-01

According to the Motivated Information Processing in Groups (MIP-G) model, groups should perform ambiguous (non-ambiguous) tasks better when they have high (low) epistemic motivation and concomitant tendencies to engage in systematic (heuristic) information processing and exchange. The authors

FY 1998 achievement report on the R and D for accelerating the basement arrangement of the biological resource information. Bioinformatics; 1998 nendo seibutsu shigen joho kiban seibi kasokuka kenkyu kaihatsu seika hokokusho. Bioinformatics

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-04-01

The paper described the FY 1998 results of the development of bioinformatics. All structure/sequence known proteins from all public databases were hierarchically classified systematically and according to similarities among sequences. Individual proteins in each classified group were added with explanatory notes of structure and physiological function. The mutually related information in metabolic system/signal transfer system was also included. The state of each residue position was classified into three states in terms of the solvent accessibility and three states in terms of the secondary structure. Parameter sets of occurrence frequency for each state of 20 kinds of amino acid were made. By these, it can be evaluated how much the arbitrary amino acid sequence is suitable for each structure in database. The data on the structure of low molecular-weight compounds are also incorporated so that the search for the related biomolecular system information becomes possible. The metabolic system/signal transfer system information was made database, the link was formed between each protein and each low molecular-weight compound, and the information on biomolecular networks was made searchable. A system to predict/support protein structure and function was developed. (NEDO)

Charge patterns as templates for the assembly of layered biomolecular structures.

Science.gov (United States)

Naujoks, Nicola; Stemmer, Andreas

2006-08-01

Electric fields are used to guide the assembly of biomolecules in predefined geometric patterns on solid substrates. Local surface charges serve as templates to selectively position proteins on thin-film polymeric electret layers, thereby creating a basis for site-directed layered assembly of biomolecular structures. Charge patterns are created using the lithographic capabilities of an atomic force microscope, namely by applying voltage pulses between a conductive tip and the sample. Samples consist of a poly(methyl methacrylate) layer on a p-doped silicon support. Subsequently, the sample is developed in a water-in-oil emulsion, consisting of a dispersed aqueous phase containing biotin-modified immunoglobulinG molecules, and a continuous nonpolar, insulating oil phase. The electrostatic fields cause a net force of (di)electrophoretic nature on the droplet, thereby guiding the proteins to the predefined locations. Due to the functionalization of the immunoglobulinG molecules with biotin-groups, these patterns can now be used to initiate the localized layer-by-layer assembly of biomolecules based on the avidin-biotin mechanism. By binding 40 nm sized biotin-labelled beads to the predefined locations via a streptavidin linker, we verify the functionality of the previously deposited immunoglobulinG-biotin. All assembly steps following the initial deposition of the immunoglobulinG from emulsion can conveniently be conducted in aqueous solutions. Results show that pattern definition is maintained after immersion into aqueous solution.

Information processing in the outer retina of fish

NARCIS (Netherlands)

Endeman, D.

2017-01-01

The retina translates light into neuronal activity. Thus, it renders visual information of the external environment. The retina can only send a limited amount of information to the brain within a given period. To use this amount optimally, light stimuli are strongly processed in the retina. This

Motivated information processing in organizational teams: Progress, puzzles, and prospects

NARCIS (Netherlands)

Nijstad, B.A.; de Dreu, C.K.W.

2012-01-01

Much of the research into group and team functioning looks at groups that perform cognitive tasks, such as decision making, problem solving, and innovation. The Motivated Information Processing in Groups Model (MIP-G; De Dreu, Nijstad, & Van Knippenberg, 2008) conjectures that information processing

Experimental design for dynamics identification of cellular processes.

Science.gov (United States)

Dinh, Vu; Rundell, Ann E; Buzzard, Gregery T

2014-03-01

We address the problem of using nonlinear models to design experiments to characterize the dynamics of cellular processes by using the approach of the Maximally Informative Next Experiment (MINE), which was introduced in W. Dong et al. (PLoS ONE 3(8):e3105, 2008) and independently in M.M. Donahue et al. (IET Syst. Biol. 4:249-262, 2010). In this approach, existing data is used to define a probability distribution on the parameters; the next measurement point is the one that yields the largest model output variance with this distribution. Building upon this approach, we introduce the Expected Dynamics Estimator (EDE), which is the expected value using this distribution of the output as a function of time. We prove the consistency of this estimator (uniform convergence to true dynamics) even when the chosen experiments cluster in a finite set of points. We extend this proof of consistency to various practical assumptions on noisy data and moderate levels of model mismatch. Through the derivation and proof, we develop a relaxed version of MINE that is more computationally tractable and robust than the original formulation. The results are illustrated with numerical examples on two nonlinear ordinary differential equation models of biomolecular and cellular processes.

Motivated information processing in group judgement and decision making

NARCIS (Netherlands)

de Dreu, C.K.W.; Nijstad, B.A.; van Knippenberg, D.

2008-01-01

This article expands the view of groups as information processors into a motivated information processing in groups (MIP-G) model by emphasizing, first, the mixedmotive structure of many group tasks and, second, the idea that individuals engage in more or less deliberate information search and

Motivated information processing, strategic choice, and the quality of negotiated agreement

NARCIS (Netherlands)

De Dreu, Carsten K W; Beersma, Bianca; Stroebe, Katherine; Euwema, Martin C.

The authors tested a motivated information-processing model of negotiation: To reach high joint outcomes, negotiators need a deep understanding of the task, which requires them to exchange information and to process new information systematically. All this depends on social motivation, epistemic

Motivated information processing, strategic choice, and the quality of negotiated agreement

NARCIS (Netherlands)

De Dreu, CKW; Beersma, B; Stroebe, K; Euwema, MC

The authors tested a motivated information-processing model of negotiation: To reach high joint outcomes, negotiators need a deep understanding of the task, which requires them to exchange information and to process new information. systematically. All this depends on social motivation, epistemic

Multidimensional biochemical information processing of dynamical patterns.

Science.gov (United States)

Hasegawa, Yoshihiko

2018-02-01

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multidimensional information from dynamical concentration patterns of signaling molecules. We herein study how biochemical systems can process multidimensional information embedded in dynamical patterns. We model the decoding networks by linear response functions, and optimize the functions with the calculus of variations to maximize the mutual information between patterns and output. We find that, when the noise intensity is lower, decoders with different linear response functions, i.e., distinct decoders, can extract much information. However, when the noise intensity is higher, distinct decoders do not provide the maximum amount of information. This indicates that, when transmitting information by dynamical patterns, embedding information in multiple patterns is not optimal when the noise intensity is very large. Furthermore, we explore the biochemical implementations of these decoders using control theory and demonstrate that these decoders can be implemented biochemically through the modification of cascade-type networks, which are prevalent in actual signaling pathways.

Proceedings of the 2nd international advisory committee on biomolecular dynamics instrument DNA in MLF at J-PARC

International Nuclear Information System (INIS)

Arai, Masatoshi; Aizawa, Kazuya; Nakajima, Kenji; Shibata, Kaoru; Takahashi, Nobuaki

2009-07-01

The 2nd International Advisory Committee on the 'Biomolecular Dynamics Backscattering Spectrometer DNA' was held on November 12th - 13th, 2008 at J-PARC Center, Japan Atomic Energy Agency. This IAC has been organized for aiming to realize an innovative neutron backscattering instrument in the Materials and Life Science Experimental Facility (MLF) at the J-PARC and therefore four leading scientists in the field of neutron backscattering instruments has been selected as the member (Dr. Dan Neumann (Chair); Prof. Ferenc Mezei; Dr. Hannu Mutka; Dr. Philip Tregenna-Piggott), and the 1st IAC had been held on February 27th - 29th, 2008. This report includes the executive summary and materials of the presentations in the 2nd IAC. (author)

Catechol-Based Hydrogel for Chemical Information Processing

Directory of Open Access Journals (Sweden)

Eunkyoung Kim

2017-07-01

Full Text Available Catechols offer diverse properties and are used in biology to perform various functions that range from adhesion (e.g., mussel proteins to neurotransmission (e.g., dopamine, and mimicking the capabilities of biological catechols have yielded important new materials (e.g., polydopamine. It is well known that catechols are also redox-active and we have observed that biomimetic catechol-modified chitosan films are redox-active and possess interesting molecular electronic properties. In particular, these films can accept, store and donate electrons, and thus offer redox-capacitor capabilities. We are enlisting these capabilities to bridge communication between biology and electronics. Specifically, we are investigating an interactive redox-probing approach to access redox-based chemical information and convert this information into an electrical modality that facilitates analysis by methods from signal processing. In this review, we describe the broad vision and then cite recent examples in which the catechol–chitosan redox-capacitor can assist in accessing and understanding chemical information. Further, this redox-capacitor can be coupled with synthetic biology to enhance the power of chemical information processing. Potentially, the progress with this biomimetic catechol–chitosan film may even help in understanding how biology uses the redox properties of catechols for redox signaling.

Aging, culture, and memory for categorically processed information.

Science.gov (United States)

Yang, Lixia; Chen, Wenfeng; Ng, Andy H; Fu, Xiaolan

2013-11-01

Literature on cross-cultural differences in cognition suggests that categorization, as an information processing and organization strategy, was more often used by Westerners than by East Asians, particularly for older adults. This study examines East-West cultural differences in memory for categorically processed items and sources in young and older Canadians and native Chinese with a conceptual source memory task (Experiment 1) and a reality monitoring task (Experiment 2). In Experiment 1, participants encoded photographic faces of their own ethnicity that were artificially categorized into GOOD or EVIL characters and then completed a source memory task in which they identified faces as old-GOOD, old-EVIL, or new. In Experiment 2, participants viewed a series of words, each followed either by a corresponding image (i.e., SEEN) or by a blank square within which they imagined an image for the word (i.e., IMAGINED). At test, they decided whether the test words were old-SEEN, old-IMAGINED, or new. In general, Canadians outperformed Chinese in memory for categorically processed information, an effect more pronounced for older than for young adults. Extensive exercise of culturally preferred categorization strategy differentially benefits Canadians and reduces their age group differences in memory for categorically processed information.

Quantum information processing and nuclear magnetic resonance

International Nuclear Information System (INIS)

Cummins, H.K.

2001-01-01

Quantum computers are information processing devices which operate by and exploit the laws of quantum mechanics, potentially allowing them to solve problems which are intractable using classical computers. This dissertation considers the practical issues involved in one of the more successful implementations to date, nuclear magnetic resonance (NMR). Techniques for dealing with systematic errors are presented, and a quantum protocol is implemented. Chapter 1 is a brief introduction to quantum computation. The physical basis of its efficiency and issues involved in its implementation are discussed. NMR quantum information processing is reviewed in more detail in Chapter 2. Chapter 3 considers some of the errors that may be introduced in the process of implementing an algorithm, and high-level ways of reducing the impact of these errors by using composite rotations. Novel general expressions for stabilising composite rotations are presented in Chapter 4 and a new class of composite rotations, tailored composite rotations, presented in Chapter 5. Chapter 6 describes some of the advantages and pitfalls of combining composite rotations. Experimental evaluations of the composite rotations are given in each case. An actual implementation of a quantum information protocol, approximate quantum cloning, is presented in Chapter 7. The dissertation ends with appendices which contain expansions of some equations and detailed calculations of certain composite rotation results, as well as spectrometer pulse sequence programs. (author)

Polarization information processing and software system design for simultaneously imaging polarimetry

Science.gov (United States)

Wang, Yahui; Liu, Jing; Jin, Weiqi; Wen, Renjie

2015-08-01

Simultaneous imaging polarimetry can realize real-time polarization imaging of the dynamic scene, which has wide application prospect. This paper first briefly illustrates the design of the double separate Wollaston Prism simultaneous imaging polarimetry, and then emphases are put on the polarization information processing methods and software system design for the designed polarimetry. Polarization information processing methods consist of adaptive image segmentation, high-accuracy image registration, instrument matrix calibration. Morphological image processing was used for image segmentation by taking dilation of an image; The accuracy of image registration can reach 0.1 pixel based on the spatial and frequency domain cross-correlation; Instrument matrix calibration adopted four-point calibration method. The software system was implemented under Windows environment based on C++ programming language, which realized synchronous polarization images acquisition and preservation, image processing and polarization information extraction and display. Polarization data obtained with the designed polarimetry shows that: the polarization information processing methods and its software system effectively performs live realize polarization measurement of the four Stokes parameters of a scene. The polarization information processing methods effectively improved the polarization detection accuracy.

Bridging domains : a comparison between information processing in Archaea and Eukarya

NARCIS (Netherlands)

Koning, de B.

2015-01-01

Bridging Domains

A Comparison between Information Processing in Archaea and Eukarya

Studying Information Processing

Living cells evolved complex systems to handle the flow of information both

Cost information in succeeding stages of the design process

NARCIS (Netherlands)

Tempelmans Plat, H.; Deiman, E.P.; Beheshti, M.R.; Zreik, K.

1993-01-01

Adequate decision making in the design process needs information about oost oonsequences over the life of the designed object. In succeeding stages the types of decisions change; as a consequence the type of oost information will differ as well. For each stage oost information about realized

Informative providing of processes of development on industrial enterprises

OpenAIRE

Kalinichenko, L.

2010-01-01

Information is definite by the basic resource of activity of enterprises. Suggestion in relation to the selection of informative subsystems of strategic, tactical, operative management is borne. The list of indexes in relation to estimation of the informative providing of functional processes of enterprise is offered.

Motivated information processing in group judgment and decision making

NARCIS (Netherlands)

De Dreu, Carsten K. W.; Nijstad, Bernard A.; van Knippenberg, Daan

This article expands the view of groups as information processors into a motivated information processing in groups (MIP-G) model by emphasizing, first, the mixed-motive structure of many group tasks and, second, the idea that individuals engage in more or less deliberate information search and

45 CFR 205.35 - Mechanized claims processing and information retrieval systems; definitions.

Science.gov (United States)

2010-10-01

... claims processing and information retrieval systems; definitions. Section 205.35 through 205.38 contain...: (a) A mechanized claims processing and information retrieval system, hereafter referred to as an automated application processing and information retrieval system (APIRS), or the system, means a system of...

Information processing correlates of a size-contrast illusion

Directory of Open Access Journals (Sweden)

Jason M Gold

2014-02-01

Full Text Available Perception is often influenced by context. A well-known class of perceptual context effects is perceptual contrast illusions, in which proximate stimulus regions interact to alter the perception of various stimulus attributes, such as perceived brightness, color and size. Although the phenomenal reality of contrast effects is well documented, in many cases the connection between these illusions and how information is processed by perceptual systems is not well understood. Here, we use noise as a tool to explore the information processing correlates of one such contrast effect: the Ebbinghaus-Titchener size-contrast illusion. In this illusion, the perceived size of a central dot is significantly altered by the sizes of a set of surrounding dots, such that the presence of larger surrounding dots tends to reduce the perceived size of the central dot (and vise-versa. In our experiments, we first replicated previous results that have demonstrated the subjective reality of the Ebbinghaus-Titchener illusion. We then used visual noise in a detection task to probe the manner in which observers processed information when experiencing the illusion. By correlating the noise with observers’ classification decisions, we found that the sizes of the surrounding contextual elements had a direct influence on the relative weight observers assigned to regions within and surrounding the central element. Specifically, observers assigned relatively more weight to the surrounding region and less weight to the central region in the presence of smaller surrounding contextual elements. These results offer new insights into the connection between the subjective experience of size-contrast illusions and their associated information processing correlates.

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

Science.gov (United States)

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

2017-03-01

A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL -1 and broad detection range of 10 pg mL -1 ≲ c BSA ≲ 100 µg mL -1 are observed. Combining this technique with predictive analyte binding models quantifies (within an order of magnitude) the number of active binding sites on functionalized MNPs. Comparative enzyme-linked immunosorbent assay (ELISA) studies are conducted, reproducing the manufacturer advertised BSA ELISA detection limits from 1 ng mL -1 ≲ c BSA ≲ 500 ng mL -1 . In addition to the increased sensitivity, broader detection range, and similar specificity, fd-FRS can be conducted in less than ≈30 min, compared to ≈4 h with ELISA. Thus, fd-FRS is shown to be a sensitive optical technique with potential to become an efficient diagnostic in the chemical and biomolecular sciences. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Information Technology in Small Medium Enterprise: Logistic and Production Processes

Directory of Open Access Journals (Sweden)

Maurizio Pighin

2017-01-01

Full Text Available This paper presents and discuss a survey which describes how small-medium enterprises (SMEs implement and use their information system with respect to their logistic and production processes. The study first describes the rationale of the research, then it identifies the characteristics of the companies and detects their general attitude towards information technology (IT. In the following section the paper presents a set of detailed processes to verify the structure and workflow of companies and how IT supports their processes. In the last part we study the influence of some company characteristics to effective use of processes and to different technological approaches, to support defined logistic and production processes. The novelty of the study and its interest, both in academic and institutional context as in the real world, resides in the opportunity to verify and understand the different attitudes of SMEs towards information technology in defining, organizing, planning and control their processes.

Computational information geometry for image and signal processing

CERN Document Server

Critchley, Frank; Dodson, Christopher

2017-01-01

This book focuses on the application and development of information geometric methods in the analysis, classification and retrieval of images and signals. It provides introductory chapters to help those new to information geometry and applies the theory to several applications. This area has developed rapidly over recent years, propelled by the major theoretical developments in information geometry, efficient data and image acquisition and the desire to process and interpret large databases of digital information. The book addresses both the transfer of methodology to practitioners involved in database analysis and in its efficient computational implementation.

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

International Nuclear Information System (INIS)

Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao

2014-01-01

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

Mathematics Education as a Proving-Ground for Information-Processing Theories.

Science.gov (United States)

Greer, Brian, Ed.; Verschaffel, Lieven, Ed.

1990-01-01

Five papers discuss the current and potential contributions of information-processing theory to our understanding of mathematical thinking as those contributions affect the practice of mathematics education. It is concluded that information-processing theories need to be supplemented in various ways to more adequately reflect the complexity of…

Information processing during NREM sleep and sleep quality in insomnia.

Science.gov (United States)

Ceklic, Tijana; Bastien, Célyne H

2015-12-01

Insomnia sufferers (INS) are cortically hyperaroused during sleep, which seems to translate into altered information processing during nighttime. While information processing, as measured by event-related potentials (ERPs), during wake appears to be associated with sleep quality of the preceding night, the existence of such an association during nighttime has never been investigated. This study aims to investigate nighttime information processing among good sleepers (GS) and INS while considering concomitant sleep quality. Following a multistep clinical evaluation, INS and GS participants underwent 4 consecutive nights of PSG recordings in the sleep laboratory. Thirty nine GS (mean age 34.56±9.02) and twenty nine INS (mean age 43.03±9.12) were included in the study. ERPs (N1, P2, N350) were recorded all night on Night 4 (oddball paradigm) during NREM sleep. Regardless of sleep quality, INS presented a larger N350 amplitude during SWS (p=0.042) while GS showed a larger N350 amplitude during late-night stage 2 sleep (p=0.004). Regardless of diagnosis, those who slept objectively well showed a smaller N350 amplitude (p=0.020) while those who slept subjectively well showed a smaller P2 (pInformation processing seems to be associated with concomitant subjective and objective sleep quality for both GS and INS. However, INS show an alteration in information processing during sleep, especially for inhibition processes, regardless of their sleep quality. Copyright © 2015 Elsevier B.V. All rights reserved.

P-Splines Using Derivative Information

KAUST Repository

Calderon, Christopher P.

2010-01-01

Time series associated with single-molecule experiments and/or simulations contain a wealth of multiscale information about complex biomolecular systems. We demonstrate how a collection of Penalized-splines (P-splines) can be useful in quantitatively summarizing such data. In this work, functions estimated using P-splines are associated with stochastic differential equations (SDEs). It is shown how quantities estimated in a single SDE summarize fast-scale phenomena, whereas variation between curves associated with different SDEs partially reflects noise induced by motion evolving on a slower time scale. P-splines assist in "semiparametrically" estimating nonlinear SDEs in situations where a time-dependent external force is applied to a single-molecule system. The P-splines introduced simultaneously use function and derivative scatterplot information to refine curve estimates. We refer to the approach as the PuDI (P-splines using Derivative Information) method. It is shown how generalized least squares ideas fit seamlessly into the PuDI method. Applications demonstrating how utilizing uncertainty information/approximations along with generalized least squares techniques improve PuDI fits are presented. Although the primary application here is in estimating nonlinear SDEs, the PuDI method is applicable to situations where both unbiased function and derivative estimates are available.

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.

A framework for information warehouse development processes

OpenAIRE

Holten, Roland

1999-01-01

Since the terms Data Warehouse and On-Line Analytical Processing were proposed by Inmon and Codd, Codd, Sally respectively the traditional ideas of creating information systems in support of management¿s decision became interesting again in theory and practice. Today information warehousing is a strategic market for any data base systems vendor. Nevertheless the theoretical discussions of this topic go back to the early years of the 20th century as far as management science and accounting the...

Why genetic information processing could have a quantum basis

Indian Academy of Sciences (India)

Unknown

Centre for Theoretical Studies and Supercomputer Education and Research Centre, ... the parent to the offspring, sensory information conveyed by the sense organ to the .... The task involved in genetic information processing is. ASSEMBLY.

Neural mechanisms of order information processing in working memory

Directory of Open Access Journals (Sweden)

Barbara Dolenc

2013-11-01

Full Text Available The ability to encode and maintain the exact order of short sequences of stimuli or events is often crucial to our ability for effective high-order planning. However, it is not yet clear which neural mechanisms underpin this process. Several studies suggest that in comparison with item recognition temporal order coding activates prefrontal and parietal brain regions. Results of various studies tend to favour the hypothesis that the order of the stimuli is represented and encoded on several stages, from primacy and recency estimates to the exact position of the item in a sequence. Different brain regions play a different role in this process. Dorsolateral prefrontal cortex has a more general role in attention, while the premotor cortex is more involved in the process of information grouping. Parietal lobe and hippocampus also play a significant role in order processing as they enable the representation of distance. Moreover, order maintenance is associated with the existence of neural oscillators that operate at different frequencies. Electrophysiological studies revealed that theta and alpha oscillations play an important role in the maintenance of temporal order information. Those EEG oscillations are differentially associated with processes that support the maintenance of order information and item recognition. Various studies suggest a link between prefrontal areas and memory for temporal order, implying that EEG neural oscillations in the prefrontal cortex may play a role in the maintenance of information on temporal order.

Information Processing and Dynamics in Minimally Cognitive Agents

Science.gov (United States)

Beer, Randall D.; Williams, Paul L.

2015-01-01

There has been considerable debate in the literature about the relative merits of information processing versus dynamical approaches to understanding cognitive processes. In this article, we explore the relationship between these two styles of explanation using a model agent evolved to solve a relational categorization task. Specifically, we…

Modeling biochemical transformation processes and information processing with Narrator

Directory of Open Access Journals (Sweden)

Palfreyman Niall M

2007-03-01

Full Text Available Abstract Background Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs, which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Results Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Conclusion Narrator is a

Developments in quantum information processing by nuclear ...

Indian Academy of Sciences (India)

qubits, the 2n energy levels of the spin-system can be treated as an n-qubit system. ... Quantum information processing; qubit; nuclear magnetic resonance quantum comput- ing. ..... The equilibrium spectrum has theoretical intensities in the ra-.

Information theory and signal transduction systems: from molecular information processing to network inference.

Science.gov (United States)

Mc Mahon, Siobhan S; Sim, Aaron; Filippi, Sarah; Johnson, Robert; Liepe, Juliane; Smith, Dominic; Stumpf, Michael P H

2014-11-01

Sensing and responding to the environment are two essential functions that all biological organisms need to master for survival and successful reproduction. Developmental processes are marshalled by a diverse set of signalling and control systems, ranging from systems with simple chemical inputs and outputs to complex molecular and cellular networks with non-linear dynamics. Information theory provides a powerful and convenient framework in which such systems can be studied; but it also provides the means to reconstruct the structure and dynamics of molecular interaction networks underlying physiological and developmental processes. Here we supply a brief description of its basic concepts and introduce some useful tools for systems and developmental biologists. Along with a brief but thorough theoretical primer, we demonstrate the wide applicability and biological application-specific nuances by way of different illustrative vignettes. In particular, we focus on the characterisation of biological information processing efficiency, examining cell-fate decision making processes, gene regulatory network reconstruction, and efficient signal transduction experimental design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Information Seeking in Uncertainty Management Theory: Exposure to Information About Medical Uncertainty and Information-Processing Orientation as Predictors of Uncertainty Management Success.

Science.gov (United States)

Rains, Stephen A; Tukachinsky, Riva

2015-01-01

Uncertainty management theory outlines the processes through which individuals cope with health-related uncertainty. Information seeking has been frequently documented as an important uncertainty management strategy. The reported study investigates exposure to specific types of medical information during a search, and one's information-processing orientation as predictors of successful uncertainty management (i.e., a reduction in the discrepancy between the level of uncertainty one feels and the level one desires). A lab study was conducted in which participants were primed to feel more or less certain about skin cancer and then were allowed to search the World Wide Web for skin cancer information. Participants' search behavior was recorded and content analyzed. The results indicate that exposure to two health communication constructs that pervade medical forms of uncertainty (i.e., severity and susceptibility) and information-processing orientation predicted uncertainty management success.

Professional development of future teacher of physical culture in informatively-educational space: information technologies in educational process

Directory of Open Access Journals (Sweden)

Dragnev Y. V.

2012-07-01

Full Text Available A role and value of informative educational space in the professional becoming of future teacher of physical culture is considered. It is well-proven that such environment is characterized: by the volume of educational services, power, intensity, set of terms. It is shown that higher professional education requires perfection of the use of information technologies, programmatic and informative providing of educational process. It is set that modern information technologies are the mean of increase of efficiency of management all of spheres of public activity. It is marked that the process of forming of informative culture needs the personally oriented and differentiated going near the choice of the teaching programs. Directions of the use of information technologies in the controlled from distance teaching are selected. The ways of intensification of educational process are recommended through the increase of interest of students to the study of concrete discipline, increase of volume of independent work, increase of closeness of educational material.

Toward theoretical understanding of the fertility preservation decision-making process: examining information processing among young women with cancer.

Science.gov (United States)

Hershberger, Patricia E; Finnegan, Lorna; Altfeld, Susan; Lake, Sara; Hirshfeld-Cytron, Jennifer

2013-01-01

Young women with cancer now face the complex decision about whether to undergo fertility preservation. Yet little is known about how these women process information involved in making this decision. The purpose of this article is to expand theoretical understanding of the decision-making process by examining aspects of information processing among young women diagnosed with cancer. Using a grounded theory approach, 27 women with cancer participated in individual, semistructured interviews. Data were coded and analyzed using constant-comparison techniques that were guided by 5 dimensions within the Contemplate phase of the decision-making process framework. In the first dimension, young women acquired information primarily from clinicians and Internet sources. Experiential information, often obtained from peers, occurred in the second dimension. Preferences and values were constructed in the third dimension as women acquired factual, moral, and ethical information. Women desired tailored, personalized information that was specific to their situation in the fourth dimension; however, women struggled with communicating these needs to clinicians. In the fifth dimension, women offered detailed descriptions of clinician behaviors that enhance or impede decisional debriefing. Better understanding of theoretical underpinnings surrounding women's information processes can facilitate decision support and improve clinical care.

Modelling of information processes management of educational complex

Directory of Open Access Journals (Sweden)

Оксана Николаевна Ромашкова

2014-12-01

Full Text Available This work concerns information model of the educational complex which includes several schools. A classification of educational complexes formed in Moscow is given. There are also a consideration of the existing organizational structure of the educational complex and a suggestion of matrix management structure. Basic management information processes of the educational complex were conceptualized.

Certainty and Uncertainty in Quantum Information Processing

OpenAIRE

Rieffel, Eleanor G.

2007-01-01

This survey, aimed at information processing researchers, highlights intriguing but lesser known results, corrects misconceptions, and suggests research areas. Themes include: certainty in quantum algorithms; the "fewer worlds" theory of quantum mechanics; quantum learning; probability theory versus quantum mechanics.

Biased information processing in the escalation paradigm: information search and information evaluation as potential mediators of escalating commitment.

Science.gov (United States)

Schultze, Thomas; Pfeiffer, Felix; Schulz-Hardt, Stefan

2012-01-01

Escalation of commitment denotes decision makers' increased reinvestment of resources in a losing course of action. Despite the relevance of this topic, little is known about how information is processed in escalation situations, that is, whether decision makers who receive negative outcome feedback on their initial decision search for and/or process information biasedly and whether these biases contribute to escalating commitment. Contrary to a widely cited study by E. J. Conlon and J. M. Parks (1987), in 3 experiments, the authors found that biases do not occur on the level of information search. Neither in a direct replication and extension of the original study with largely increased test power (Experiment 1) nor under methodologically improved conditions (Experiments 2 and 3) did decision makers responsible for failure differ from nonresponsible decision makers with regards to information search, and no selective search for information supporting the initial decision or voting for further reinvestment was observed. However, Experiments 3 and 4 show that the evaluation of the previously sought information is biased among participants who were responsible for initiating the course of action. Mediation analyses show that this evaluation bias in favor of reinvestment partially mediated the responsibility effect on escalation of commitment.

Crosstalk between endophytes and a plant host within information-processing networks

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Kozyrovska N. O.

2013-05-01

Full Text Available Plants are heavily populated by pro- and eukaryotic microorganisms and represent therefore the tremendous complexity as a biological system. This system exists as an information-processing entity with rather complex processes of communication, occurring throughout the individual plant. The plant cellular information-proces- sing network constitutes the foundation for processes like growth, defense, and adaptation to the environment. Up to date, the molecular mechanisms, underlying perception, transfer, analysis, and storage of the endogenous and environmental information within the plant, remain to be fully understood. The associated microorganisms and their investment in the information conditioning are often ignored. Endophytes as plant partners are indispen- sable integrative part of the plant system. Diverse endophytic microorganisms comprise «normal» microbiota that plays a role in plant immunity and helps the plant system to survive in the environment (providing assistance in defense, nutrition, detoxification etc.. The role of endophytic microbiota in the processing of information may be presumed, taking into account a plant-microbial co-evolution and empirical data. Since the literature are be- ginning to emerge on this topic, in this article, I review key works in the field of plant-endophytes interactions in the context of information processing and represent the opinion on their putative role in plant information web under defense and the adaptation to changed conditions.

Construction Of A Computerised Information-Processing Test Battery

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Johann M. Schepers

2002-09-01

Full Text Available The primary goal of the study was to construct a computerised information-processing test battery to measure choice reaction time for up to and including six bits of information, to measure discrimination reaction time with regard to colour patterns and form patterns, to measure rate of information processing with regard to perceptual stimuli and conceptual reasoning, and to develop a suitable scoring system for the respective tests. The battery of tests was applied to 58 pilots. Opsomming Die hoofdoel van die studie was om ‘n gerekenariseerde inligtingverwerkingstoets-battery te konstrueer om keusereaksietyd tot en met ses bis inligting te meet, om diskriminasie-reaksietyd ten opsigte van kleurpatrone en vormpatrone te meet, om tempo van inligtingverwerking ten opsigte van perseptuele stimuli en konseptuele redenering te meet en om ‘n gepaste nasienstelsel vir die onderskeie toetse te ontwikkel. Die battery toetse is op 58 vlieëniers toegepas

Biomolecular and structural analyses of cauliflower-like DNAs by ultraviolet, circular dichroism, and fluorescence spectroscopies in comparison with natural DNA.

Science.gov (United States)

Gill, Pooria; Ranjbar, Bijan; Saber, Reza; Khajeh, Khosro; Mohammadian, Mehdi

2011-07-01

Cauliflower-like DNAs are stem-loop DNAs that are fabricated periodically in inverted repetitions from deoxyribonucleic acid phosphates (dNTPs) by loop-mediated isothermal amplification (LAMP). Cauliflower-like DNAs have ladder-shape behaviors on gel electrophoresis, and increasing the time of LAMP leads to multiplying the repetitions, stem-loops, and electrophoretic bands. Cauliflower-like DNAs were fabricated via LAMP using two loop primers, two bumper primers, dNTPs, a λ-phage DNA template, and a Bst DNA polymerase in 75- and 90-min periods. These times led to manufacturing two types of cauliflower-like DNAs with different contents of inverted repetitions and stem-loops, which were clearly indicated by two comparable electrophoresis patterns in agarose gel. LAMP-fabricated DNAs and natural dsB-DNA (salmon genomic DNA) were dialyzed in Gomori phosphate buffer (10 mM, pH 7.4) to be isolated from salts, nucleotides, and primers. Dialyzed DNAs were studied using UV spectroscopy, circular dichroism spectropolarimetry, and fluorescence spectrophotometry. Structural analyses indicated reduction of the molecular ellipticity and extinction coefficients in comparison with B-DNA. Also, cauliflower-like DNAs demonstrated less intrinsic and more extrinsic fluorescence in comparison with natural DNA. The overwinding and lengthening of the cauliflower-like configurations of LAMP DNAs led to changes in physical parameters of this type of DNA in comparison with natural DNA. The results obtained introduced new biomolecular characteristics of DNA macromolecules fabricated within a LAMP process and show the effects of more inverted repeats and stem-loops, which are manufactured by lengthening the process.

The cognitive viewpoint on information science and processing information in cognitive psychology - a vision for interdisciplinary

Directory of Open Access Journals (Sweden)

Shirley Guimarães Pimenta

2012-08-01

Full Text Available The interaction amongst the ‘user’, ‘information’, and ‘text’ is of interest to Information Science although it has deserved insufficient attention in the literature. This issue is addressed by this paper whose main purpose is to contribute to the discussion of theoretical affinity between the cognitive viewpoint in Information Science and the information processing approach in Cognitive Psychology. Firstly, the interdisciplinary nature of Information Science is discussed and justified as a means to deepen and strengthen its theoretical framework. Such interdisciplinarity helps to avoid stagnation and keep pace with other disciplines. Secondly, the discussion takes into consideration the cognitive paradigm, which originates the cognitive viewpoint approach in Information Science. It is highlighted that the cognitive paradigm represented a change in the Social Sciences due to the shift of focus from the object and the signal to the individual. Besides that, it sheds light to the notion of models of worlds, i.e., the systems of categories and concepts that guide the interaction between the individual and his/her environment. Thirdly, the theoretical assumptions of the cognitive viewpoint approach are discussed, with emphasis on the concept of ‘information’, as resulting of cognitive processes and as related to the notion of ‘text’. This approach points out the relevance of understanding the interaction amongst users, information, and text. However, it lacks further development. Using notions which are common to both approaches, some of the gaps can be fulfilled. Finally, the concept of ‘text’, its constituents and structures are presented from the perspective of text comprehension models and according to the information processing approach. As a concluding remark, it is suggested that bringing together the cognitive viewpoint and the information processing approach can be enriching and fruitful to the both Information

Process Information System - Nuclear Power Plant Krsko

International Nuclear Information System (INIS)

Mandic, D.; Barbic, B.; Linke, B.; Colak, I.

1998-01-01

Original NEK design was using several Process Computer Systems (PCS) for both process control and process supervision. PCS were built by different manufacturers around different hardware and software platforms. Operational experience and new regulatory requirements imposed new technical and functional requirements on the PCS. Requirements such as: - Acquisition of new signals from the technological processes and environment - Implementation of new application programs - Significant improvement of MMI (Man Machine Interface) - Process data transfer to other than Main Control Room (MCR) locations - Process data archiving and capability to retrieve same data for future analysis were impossible to be implemented within old systems. In order to satisfy new requirements, NEK has decided to build new Process Information System (PIS). During the design and construction of the PIS Project Phase I, in addition to the main foreign contractor, there was significant participation of local architect engineering and construction companies. This paper presents experience of NEK and local partners. (author)

Information processing in decision-making systems.

Science.gov (United States)

van der Meer, Matthijs; Kurth-Nelson, Zeb; Redish, A David

2012-08-01

Decisions result from an interaction between multiple functional systems acting in parallel to process information in very different ways, each with strengths and weaknesses. In this review, the authors address three action-selection components of decision-making: The Pavlovian system releases an action from a limited repertoire of potential actions, such as approaching learned stimuli. Like the Pavlovian system, the habit system is computationally fast but, unlike the Pavlovian system permits arbitrary stimulus-action pairings. These associations are a "forward'' mechanism; when a situation is recognized, the action is released. In contrast, the deliberative system is flexible but takes time to process. The deliberative system uses knowledge of the causal structure of the world to search into the future, planning actions to maximize expected rewards. Deliberation depends on the ability to imagine future possibilities, including novel situations, and it allows decisions to be taken without having previously experienced the options. Various anatomical structures have been identified that carry out the information processing of each of these systems: hippocampus constitutes a map of the world that can be used for searching/imagining the future; dorsal striatal neurons represent situation-action associations; and ventral striatum maintains value representations for all three systems. Each system presents vulnerabilities to pathologies that can manifest as psychiatric disorders. Understanding these systems and their relation to neuroanatomy opens up a deeper way to treat the structural problems underlying various disorders.

ADMINISTRATION OF THE INFORMATION AND THE PROCESS OF BANK NEGOTIATION

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Almir Lindemann

2009-07-01

Full Text Available This paper analyzes the quality of the administration of information, identifying deficiencies in the information systems, used in the negotiation process for concession of bank credit, to small and mid-sized companies, under the business managers' perspective. The results make the deficiencies evident and confirm the need for change in the systems of administration of information, in order to allow for both an improvement in the negotiation process of bank credit as well as a larger economical efficiency of the available resources.

Process-aware information systems for emergency management

NARCIS (Netherlands)

Leoni, de M.; Marrella, A.; Russo, A.; Cezon, M.; Wolfsthal, Y.

2011-01-01

Nowadays, Process-aware Information Systems (PAISs) are widely used in many business scenarios, e.g., by government agencies, by insurance companies, and by banks. Despite this widespread usage, the typical application of such systems is predominantly in the context of business scenarios.