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Sample records for mesoscopic biological test

  1. Cosmic heavy ion tracks in mesoscopic biological test objects

    NASA Technical Reports Server (NTRS)

    Facius, R.

    1994-01-01

    Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on 'HZE particle effects in manned spaced flight', it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to 'large' fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated. Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too ('The BIOSTACK as an approach to high LET radiation research'), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions' trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series. Since biological investigations and physical measurements of particle tracks had to be performed in laboratories widely separated, the preferred fixed contact between biological test objects and the particle detectors

  2. Cosmic heavy ion tracks in mesoscopic biological test objects

    SciTech Connect

    Facius, R.

    1994-12-31

    Since more than 20 years ago, when the National Academy of Sciences and the National Research Council of the U.S.A. released their report on `HZE particle effects in manned spaced flight`, it has been emphasized how difficult - if not even impossible - it is to assess their radiobiological impact on man from conventional studies where biological test organisms are stochastically exposed to `large` fluences of heavy ions. An alternative, competing approach had been realized in the BIOSTACK experiments, where the effects of single cosmic as well as accelerator - heavy ions on individual biological test organisms could be investigated. Although presented from the beginning as the preferable approach for terrestrial investigations with accelerator heavy ions too (`The BIOSTACK as an approach to high LET radiation research`), only recently this insight is gaining more widespread recognition. In space flight experiments, additional constraints imposed by the infrastructure of the vehicle or satellite further impede such investigations. Restrictions concern the physical detector systems needed for the registration of the cosmic heavy ions` trajectories as well as the biological systems eligible as test organisms. Such optimized procedures and techniques were developed for the investigations on chromosome aberrations induced by cosmic heavy ions in cells of the stem meristem of lettuce seeds (Lactuca sativa) and for the investigation of the radiobiological response of Wolffia arriza, which is the smallest flowering (water) plant. The biological effects were studied by the coworkers of the Russian Institute of Biomedical Problems (IBMP) which in cooperation with the European Space Agency ESA organized the exposure in the Biosatellites of the Cosmos series.

  3. Visibility Equalizer Cutaway Visualization of Mesoscopic Biological Models

    PubMed Central

    Le Muzic, M.; Mindek, P.; Sorger, J.; Autin, L.; Goodsell, D.; Viola, I.

    2017-01-01

    In scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine-tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer-based approach for visibility specification was valuable and effective for both, scientific and educational purposes. PMID:28344374

  4. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry.

    PubMed

    Kalay, Ziya

    2011-08-01

    How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.

  5. Reconstruction of fluorescence distribution hidden in biological tissue using mesoscopic epifluorescence tomography

    NASA Astrophysics Data System (ADS)

    Björn, Saskia; Englmeier, Karl-Hans; Ntziachristos, Vasilis; Schulz, Ralf

    2011-04-01

    Mesoscopic epifluorescence tomography is a novel technique that discovers fluorescence bio-distribution in small animals by tomographic means in reflectance geometry. A collimated laser beam is scanned over the skin surface to excite fluorophores hidden within the tissue while a CCD camera acquires an image of the fluorescence emission for each source position. This configuration is highly efficient in the visible spectrum range where trans-illumination imaging of small animals is not feasible due to the high tissue absorption and scattering in biological organisms. The reconstruction algorithm is similar to the one used in fluorescence molecular tomography. However, diffusion theory cannot be employed since the source-detector separation for most image pixels is comparable to or below the scattering length of the tissue. Instead Monte Carlo simulations are utilized to predict the sensitivity functions. In a phantom study we show the effect of using enhanced source grid arrangements during the data acquisition and the reconstruction process to minimize boundary artefacts. Furthermore, we present ex vivo data that show high spatial resolution and quantitative accuracy in heterogeneous tissues using GFP-like fluorescence in B6-albino mice up to a depth of 1100 μm.

  6. cellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology

    PubMed Central

    Johnson, Graham T.; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

    2014-01-01

    cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10−7–10−8m) between molecular and cellular biology. cellPACK’s modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive 3D models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is currently available as open source code, with tools for validation of models and with recipes and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators, and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org. PMID:25437435

  7. cellPACK: a virtual mesoscope to model and visualize structural systems biology.

    PubMed

    Johnson, Graham T; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S; Sanner, Michel F; Olson, Arthur J

    2015-01-01

    cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10-100 nm) between molecular and cellular biology scales. cellPACK's modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive three-dimensional models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is available as open-source code, with tools for validation of models and with 'recipes' and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org/.

  8. Mesoscopic neurodynamics.

    PubMed

    Kiss, Tamás; Erdi, Péter

    2002-01-01

    An overview is given on the history, theory, and applications of mesoscopic neural models. It is shown why and how we can describe the behavior of a large population of neurons by the method of statistical neurodynamics. Normal and epileptic propagation of cortical activity have been simulated.

  9. ENGINEERING BULLETIN: BIOLOGICAL TOXICITY TESTING

    EPA Science Inventory

    This Engineering Bulletin is intended to provide site managers with information on ecological assessment and biological toxicity testing, applicability of biological toxicity testing, planning effective biological toxicity assessments, descriptions of test methods, limitations, c...

  10. Mesoscopic Lawlessness

    NASA Astrophysics Data System (ADS)

    Laughlin, R. B.

    2012-02-01

    Whether physics will contribute significantly to unraveling the secrets of life, the grandest challenge of them all, depends critically on whether proteins and other mesoscale objects exhibit emergent law. By this I mean quantitative relationships among their measured properties that are always true. The jury is still out on the matter, for there is evidence both for and against, but it is spotty, on account of the difficulty of measuring 100 nm - 1000 objects without damaging them quantum mechanically. It is therefore not clear that history will repeat itself. Physics contributed mightily to 20th century materials science through its identification and mastery of powerful macroscopic emergent laws such as crystalline rigidity, superconductivity and ferromagnetism, but it cannot do the same thing in biology, regardless of how powerful computers get, unless nature cooperates. The challenge before us as physicists is therefore not to amass more and more terabytes of data and computational output but rather to search for and, with luck, find operating principles at the scale of life greater than those of chemistry, which is to say, greater than a world ruled by nothing but miraculous accidents.

  11. Testing multiple biological mediators simultaneously.

    PubMed

    Boca, Simina M; Sinha, Rashmi; Cross, Amanda J; Moore, Steven C; Sampson, Joshua N

    2014-01-15

    Modern biomedical and epidemiological studies often measure hundreds or thousands of biomarkers, such as gene expression or metabolite levels. Although there is an extensive statistical literature on adjusting for 'multiple comparisons' when testing whether these biomarkers are directly associated with a disease, testing whether they are biological mediators between a known risk factor and a disease requires a more complex null hypothesis, thus offering additional methodological challenges. We propose a permutation approach that tests multiple putative mediators and controls the family wise error rate. We demonstrate that, unlike when testing direct associations, replacing the Bonferroni correction with a permutation approach that focuses on the maximum of the test statistics can significantly improve the power to detect mediators even when all biomarkers are independent. Through simulations, we show the power of our method is 2-5× larger than the power achieved by Bonferroni correction. Finally, we apply our permutation test to a case-control study of dietary risk factors and colorectal adenoma to show that, of 149 test metabolites, docosahexaenoate is a possible mediator between fish consumption and decreased colorectal adenoma risk. R-package included in online Supplementary Material.

  12. Electron waiting times for the mesoscopic capacitor

    NASA Astrophysics Data System (ADS)

    Hofer, Patrick P.; Dasenbrook, David; Flindt, Christian

    2016-08-01

    We evaluate the distribution of waiting times between electrons emitted by a driven mesoscopic capacitor. Based on a wave packet approach we obtain analytic expressions for the electronic waiting time distribution and the joint distribution of subsequent waiting times. These semi-classical results are compared to a full quantum treatment based on Floquet scattering theory and good agreement is found in the appropriate parameter ranges. Our results provide an intuitive picture of the electronic emissions from the driven mesoscopic capacitor and may be tested in future experiments.

  13. Automatic interpretation of biological tests.

    PubMed

    Boufriche-Boufaïda, Z

    1998-03-01

    In this article, an approach for an Automatic Interpretation of Biological Tests (AIBT) is described. The developed system is much needed in Preventive Medicine Centers (PMCs). It is designed as a self-sufficient system that could be easily used by trained nurses during the routine visit. The results that the system provides are not only useful to provide the PMC physicians with a preliminary diagnosis, but also allows them more time to focus on the serious cases, making the clinical visit more qualitative. On the other hand, because the use of such a system has been planned for many years, its possibilities for future extensions must be seriously considered. The methodology adopted can be interpreted as a combination of the advantages of two main approaches adopted in current diagnostic systems: the production system approach and the object-oriented system approach. From the rules, the ability of these approaches to capture the deductive processes of the expert in domains where causal mechanisms are often understood are retained. The object-oriented approach guides the elicitation and the engineering of knowledge in such a way that abstractions, categorizations and classifications are encouraged whilst individual instances of objects of any type are recognized as separate, independent entities.

  14. Apparatus for automated testing of biological specimens

    DOEpatents

    Layne, Scott P.; Beugelsdijk, Tony J.

    1999-01-01

    An apparatus for performing automated testing of infections biological specimens is disclosed. The apparatus comprise a process controller for translating user commands into test instrument suite commands, and a test instrument suite comprising a means to treat the specimen to manifest an observable result, and a detector for measuring the observable result to generate specimen test results.

  15. Mesoscopic Interferometers for Electron Waves

    SciTech Connect

    Rohrlich, D.

    2005-09-15

    Mesoscopic interferometers are electronic analogues of optical interferometers, with 'quantum point contacts' playing the role of optical beam splitters. Mesoscopic analogues of two-slit, Mach-Zehnder and Fabry-Perot interferometers have been built. A fundamental difference between electron and photon interferometry is that electron interferometry is nonlocal.

  16. Biomonitoring test procedures and biological criteria

    SciTech Connect

    Kszos, L.A.; Lipschultz, M.J.; Foster, W.E.

    1997-10-01

    The Water Environment Federation recently issued a special publication, Biomonitoring in the Water Environment. In this paper, the authors highlight the contents of the chapter 3, Biomonitoring Test Procedures, identify current trends in test procedures and introduce the concept of biological criteria (biocriteria). The book chapter (and this paper) focuses on freshwater and marine chronic and acute toxicity tests used in the National Pollutant Discharge Elimination System (NPDES) permits program to identify effluents and receiving waters containing toxic materials in acutely or chronically toxic concentrations. The two major categories of toxicity tests include acute tests and chronic tests. The USEPA chronic tests required in NPDEs permits have been shortened to 7 days by focusing on the most sensitive life-cycle stages; these tests are often referred to as short-term chronic tests. The type of test(s) required depend on NPDES permit requirements, objectives of the test, available resources, requirements of the test organisms, and effluent characteristics such as variability in flow or toxicity. The permit writer will determine the requirements for toxicity test(s) by considering such factors as dilution, effluent variability, and exposure variability. Whether the required test is acute or chronic, the objective of the test is to estimate the safe or no effect concentration which is defined as the concentration which will permit normal propagation of fish and other aquatic life in the receiving waters. In this paper, the authors review the types of toxicity tests, the commonly used test organisms, and the uses of toxicity test data. In addition, they briefly describe research on new methods and the use of biological criteria.

  17. Mesoscopic supersolid of dipoles in a trap

    SciTech Connect

    Golomedov, A. E.; Astrakharchik, G. E.; Lozovik, Yu. E.

    2011-09-15

    A mesoscopic system of dipolar bosons trapped by a harmonic potential is considered. The system has a number of physical realizations including dipole excitons, atoms with large dipolar moment, polar molecules, and Rydberg atoms in inhomogeneous electric field. We carry out a diffusion Monte Carlo simulation to define the quantum properties of a two-dimensional system of trapped dipoles at zero temperature. In dimensionless units the system is described by two control parameters, namely, the number of particles and the strength of the interparticle interaction. We have shown that when the interparticle interaction is strong enough a mesoscopic crystal is formed. As the strength of interactions is decreased a multistage melting takes place. Off-diagonal order in the system is tested using natural-orbitals analysis. We have found that the system might be Bose condensed even in the case of strong interparticle interactions. There is a set of parameters for which a spatially ordered structure is formed while simultaneously the fraction of Bose-condensed particles is nonzero. This might be considered as a realization of a mesoscopic supersolid.

  18. Nonequilibrium mesoscopic conductance fluctuations

    NASA Astrophysics Data System (ADS)

    Ludwig, T.; Blanter, Ya. M.; Mirlin, A. D.

    2004-12-01

    We investigate the amplitude of mesoscopic fluctuations of the differential conductance of a metallic wire at arbitrary bias voltage V . For noninteracting electrons, the variance ⟨δg2⟩ increases with V . The asymptotic large- V behavior is ⟨δg2⟩˜V/Vc (where eVc=D/L2 is the Thouless energy), in agreement with the earlier prediction by Larkin and Khmelnitskii. We find, however, that this asymptotics has a very small numerical prefactor and sets in at very large V/Vc only, which strongly complicates its experimental observation. This high-voltage behavior is preceded by a crossover regime, V/Vc≲30 , where the conductance variance increases by a factor ˜3 as compared to its value in the regime of universal conductance fluctuations (i.e., at V→0 ). We further analyze the effect of dephasing due to the electron-electron scattering on ⟨δg2⟩ at high voltages. With the Coulomb interaction taken into account, the amplitude of conductance fluctuations becomes a nonmonotonic function of V . Specifically, ⟨δg2⟩ drops as 1/V for voltages V≫gVc , where g is the dimensionless conductance. In this regime, the conductance fluctuations are dominated by quantum-coherent regions of the wire adjacent to the reservoirs.

  19. Mesoscopic quantum cryptography

    NASA Astrophysics Data System (ADS)

    Molotkov, S. N.

    2017-03-01

    Since a strictly single-photon source is not yet available, in quantum cryptography systems, one uses, as information quantum states, coherent radiation of a laser with an average number of photons of μ ≈ 0.1-0.5 in a pulse, attenuated to the quasi-single-photon level. The linear independence of a set of coherent quasi-single-photon information states leads to the possibility of unambiguous measurements that, in the presence of losses in the line, restrict the transmission range of secret keys. Starting from a certain value of critical loss (the length of the line), the eavesdropper knows the entire key, does not make errors, and is not detected—the distribution of secret keys becomes impossible. This problem is solved by introducing an additional reference state with an average number of photons of μcl ≈ 103-106, depending on the length of the communication line. It is shown that the use of a reference state does not allow the eavesdropper to carry out measurements with conclusive outcome while remaining undetected. A reference state guarantees detecting an eavesdropper in a channel with high losses. In this case, information states may contain a mesoscopic average number of photons in the range of μ q ≈ 0.5-102. The protocol proposed is easy to implement technically, admits flexible adjustment of parameters to the length of the communication line, and is simple and transparent for proving the secrecy of keys.

  20. Mesoscopic simulations of recrystallization

    SciTech Connect

    Holm, E.A.; Rollett, A.D.; Srolovitz, D.J.

    1995-08-01

    The application of computer simulation to grain growth and recrystallization was strongly stimulated in the early 80s by the realization that Monte Carlo models could be applied to problems of grain structure evolution. By extension of the Ising model for domain modeling of magnetic domains to the Potts model (with generalized spin numbers) it was then possible to represent discretely grains (domains) by regions of similarly oriented sets of material (lattice) points. In parallel with this fascinating development, there also occured notable work on analytical models, especially by Abbruzzese and Bunge, which has been particularly useful for understanding the variation of texture (crystallographic preferred orientation) during grain growth processes. Geometric models of recrystallization, worked on most recently and productively by Nes et al., have been useful in connection with grain size prediction as a result of recrystallization. Also, mesh-based models have been developed to a high degree by Kawasaki, Fradkov and others, and, rather recently, by Humphreys to model not just grain growth but also the nucleation process in recrystallization. These models have the strength that they deal with the essential features of grains, i.e. the nodes, but have some limitations when second phases must be considered. These various approaches to modeling of recrystallization processes will be reviewed, with a special emphasis on practical approaches to implementing the Potts model. This model has been remarkably successful in modeling such diverse phenomena as dynamic recrystallization, secondary recrystallization (abnormal grain growth), particle-inhibited recrystallization, and grain structure evolution in soldering and welding. In summary, the application of mesoscopic simulation to the phenomenon of recrystallization has yielded much new insight into some longstanding deficiencies in our understanding.

  1. Quantum fluctuations in mesoscopic systems

    NASA Astrophysics Data System (ADS)

    Benatti, F.; Carollo, F.; Floreanini, R.; Narnhofer, H.

    2017-10-01

    Recent experimental results point to the existence of coherent quantum phenomena in systems made of a large number of particles, despite the fact that for many-body systems the presence of decoherence is hardly negligible and emerging classicality is expected. This behaviour hinges on collective observables, named quantum fluctuations, that retain a quantum character even in the thermodynamic limit: they provide useful tools for studying properties of many-body systems at the mesoscopic level, in-between the quantum microscopic scale and the classical macroscopic one. We herein present the general theory of quantum fluctuations in mesoscopic systems, and study their dynamics in a quantum open system setting, taking into account the unavoidable effects of dissipation and noise induced by the external environment. As in the case of microscopic systems, decoherence is not always the only dominating effect at the mesoscopic scale: certain types of environment can provide means for entangling collective fluctuations through a purely noisy mechanism.

  2. Unit testing, model validation, and biological simulation

    PubMed Central

    Watts, Mark D.; Ghayoomie, S. Vahid; Larson, Stephen D.; Gerkin, Richard C.

    2016-01-01

    The growth of the software industry has gone hand in hand with the development of tools and cultural practices for ensuring the reliability of complex pieces of software. These tools and practices are now acknowledged to be essential to the management of modern software. As computational models and methods have become increasingly common in the biological sciences, it is important to examine how these practices can accelerate biological software development and improve research quality. In this article, we give a focused case study of our experience with the practices of unit testing and test-driven development in OpenWorm, an open-science project aimed at modeling Caenorhabditis elegans. We identify and discuss the challenges of incorporating test-driven development into a heterogeneous, data-driven project, as well as the role of model validation tests, a category of tests unique to software which expresses scientific models. PMID:27635225

  3. Quasi-Low-Dimensional Electron Gas with One Populated Band as a Testing Ground for Time-Dependent Density-Functional Theory of Mesoscopic Systems

    NASA Astrophysics Data System (ADS)

    Nazarov, Vladimir U.

    2017-06-01

    We find an exact analytical solution to the exchange-only time-dependent density-functional theory (TDDFT) problem for a significant class of quasi-low-dimensional (QLD) materials: QLD electron gas with only one band filled in the direction perpendicular to the layer or wire. The theory yields the TD exchange potential as an explicit nonlocal operator of the TD spin density. The dressed interband (image states) excitation spectra of quasi-two-dimensional electron gas are obtained, while the comparison with the Kohn-Sham transitions provides insights into the qualitative and quantitative role of the many-body interactions. Important cancellations between the Hartree fH and the exchange fx kernels of TDDFT are found in the low-density regime, elucidating the interrelations between the Kohn-Sham and the many-body dynamics in mesoscopic systems.

  4. Quasi-Low-Dimensional Electron Gas with One Populated Band as a Testing Ground for Time-Dependent Density-Functional Theory of Mesoscopic Systems.

    PubMed

    Nazarov, Vladimir U

    2017-06-09

    We find an exact analytical solution to the exchange-only time-dependent density-functional theory (TDDFT) problem for a significant class of quasi-low-dimensional (QLD) materials: QLD electron gas with only one band filled in the direction perpendicular to the layer or wire. The theory yields the TD exchange potential as an explicit nonlocal operator of the TD spin density. The dressed interband (image states) excitation spectra of quasi-two-dimensional electron gas are obtained, while the comparison with the Kohn-Sham transitions provides insights into the qualitative and quantitative role of the many-body interactions. Important cancellations between the Hartree f_{H} and the exchange f_{x} kernels of TDDFT are found in the low-density regime, elucidating the interrelations between the Kohn-Sham and the many-body dynamics in mesoscopic systems.

  5. What can we learn from noise? - Mesoscopic nonequilibrium statistical physics.

    PubMed

    Kobayashi, Kensuke

    2016-01-01

    Mesoscopic systems - small electric circuits working in quantum regime - offer us a unique experimental stage to explorer quantum transport in a tunable and precise way. The purpose of this Review is to show how they can contribute to statistical physics. We introduce the significance of fluctuation, or equivalently noise, as noise measurement enables us to address the fundamental aspects of a physical system. The significance of the fluctuation theorem (FT) in statistical physics is noted. We explain what information can be deduced from the current noise measurement in mesoscopic systems. As an important application of the noise measurement to statistical physics, we describe our experimental work on the current and current noise in an electron interferometer, which is the first experimental test of FT in quantum regime. Our attempt will shed new light in the research field of mesoscopic quantum statistical physics.

  6. Reaction rates for mesoscopic reaction-diffusion kinetics

    DOE PAGES

    Hellander, Stefan; Hellander, Andreas; Petzold, Linda

    2015-02-23

    The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In thismore » paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. Finally, we show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.« less

  7. Reaction rates for mesoscopic reaction-diffusion kinetics

    SciTech Connect

    Hellander, Stefan; Hellander, Andreas; Petzold, Linda

    2015-02-23

    The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. Finally, we show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.

  8. Prospective Tests on Biological Models of Acupuncture

    PubMed Central

    2009-01-01

    The biological effects of acupuncture include the regulation of a variety of neurohumoral factors and growth control factors. In science, models or hypotheses with confirmed predictions are considered more convincing than models solely based on retrospective explanations. Literature review showed that two biological models of acupuncture have been prospectively tested with independently confirmed predictions: The neurophysiology model on the long-term effects of acupuncture emphasizes the trophic and anti-inflammatory effects of acupuncture. Its prediction on the peripheral effect of endorphin in acupuncture has been confirmed. The growth control model encompasses the neurophysiology model and suggests that a macroscopic growth control system originates from a network of organizers in embryogenesis. The activity of the growth control system is important in the formation, maintenance and regulation of all the physiological systems. Several phenomena of acupuncture such as the distribution of auricular acupuncture points, the long-term effects of acupuncture and the effect of multimodal non-specific stimulation at acupuncture points are consistent with the growth control model. The following predictions of the growth control model have been independently confirmed by research results in both acupuncture and conventional biomedical sciences: (i) Acupuncture has extensive growth control effects. (ii) Singular point and separatrix exist in morphogenesis. (iii) Organizers have high electric conductance, high current density and high density of gap junctions. (iv) A high density of gap junctions is distributed as separatrices or boundaries at body surface after early embryogenesis. (v) Many acupuncture points are located at transition points or boundaries between different body domains or muscles, coinciding with the connective tissue planes. (vi) Some morphogens and organizers continue to function after embryogenesis. Current acupuncture research suggests a convergence

  9. Mesoscopic model for binary fluids

    NASA Astrophysics Data System (ADS)

    Echeverria, C.; Tucci, K.; Alvarez-Llamoza, O.; Orozco-Guillén, E. E.; Morales, M.; Cosenza, M. G.

    2017-10-01

    We propose a model for studying binary fluids based on the mesoscopic molecular simulation technique known as multiparticle collision, where the space and state variables are continuous, and time is discrete. We include a repulsion rule to simulate segregation processes that does not require calculation of the interaction forces between particles, so binary fluids can be described on a mesoscopic scale. The model is conceptually simple and computationally efficient; it maintains Galilean invariance and conserves the mass and energy in the system at the micro- and macro-scale, whereas momentum is conserved globally. For a wide range of temperatures and densities, the model yields results in good agreement with the known properties of binary fluids, such as the density profile, interface width, phase separation, and phase growth. We also apply the model to the study of binary fluids in crowded environments with consistent results.

  10. DNA-programmed mesoscopic architecture

    NASA Astrophysics Data System (ADS)

    Halverson, Jonathan D.; Tkachenko, Alexei V.

    2013-06-01

    We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs that are directionally functionalized with DNA. The combination of directionality and selectivity of interactions allows one to avoid unwanted metastable configurations, which have been shown to lead to slow self-assembly kinetics even in much simpler systems. With numerical simulations, we show that a variety of target mesoscopic objects can be designed and self-assembled in near perfect yield. They include cubes, pyramids, boxes, and even an Empire State Building model. We summarize our findings with a set of design strategies that leads to the successful self-assembly of a wide range of mesostructures.

  11. DNA-programmed mesoscopic architecture.

    PubMed

    Halverson, Jonathan D; Tkachenko, Alexei V

    2013-06-01

    We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs that are directionally functionalized with DNA. The combination of directionality and selectivity of interactions allows one to avoid unwanted metastable configurations, which have been shown to lead to slow self-assembly kinetics even in much simpler systems. With numerical simulations, we show that a variety of target mesoscopic objects can be designed and self-assembled in near perfect yield. They include cubes, pyramids, boxes, and even an Empire State Building model. We summarize our findings with a set of design strategies that leads to the successful self-assembly of a wide range of mesostructures.

  12. Mesoscopic Superposition States in Relativistic Landau Levels

    SciTech Connect

    Bermudez, A.; Martin-Delgado, M. A.; Solano, E.

    2007-09-21

    We show that a linear superposition of mesoscopic states in relativistic Landau levels can be built when an external magnetic field couples to a relativistic spin 1/2 charged particle. Under suitable initial conditions, the associated Dirac equation produces unitarily superpositions of coherent states involving the particle orbital quanta in a well-defined mesoscopic regime. We demonstrate that these mesoscopic superpositions have a purely relativistic origin and disappear in the nonrelativistic limit.

  13. Raise Test Scores: Integrate Biology and Calculus.

    ERIC Educational Resources Information Center

    Lukens, Jeffrey D.; Feinstein, Sheryl

    This paper presents the results of research that compared the academic achievement of high school students enrolled in an integrated Advanced Placement Biology/Advanced Placement Calculus course with students enrolled in traditional Advanced Placement Biology and Advanced Placement Calculus courses. Study subjects included high school students…

  14. Mesoscopic Simulations of Crosslinked Polymer Networks

    NASA Astrophysics Data System (ADS)

    Megariotis, Grigorios; Vogiatzis, Georgios G.; Schneider, Ludwig; Müller, Marcus; Theodorou, Doros N.

    2016-08-01

    A new methodology and the corresponding C++ code for mesoscopic simulations of elastomers are presented. The test system, crosslinked ds-1’4-polyisoprene’ is simulated with a Brownian Dynamics/kinetic Monte Carlo algorithm as a dense liquid of soft, coarse-grained beads, each representing 5-10 Kuhn segments. From the thermodynamic point of view, the system is described by a Helmholtz free-energy containing contributions from entropic springs between successive beads along a chain, slip-springs representing entanglements between beads on different chains, and non-bonded interactions. The methodology is employed for the calculation of the stress relaxation function from simulations of several microseconds at equilibrium, as well as for the prediction of stress-strain curves of crosslinked polymer networks under deformation.

  15. Statistics and Hypothesis Testing in Biology.

    ERIC Educational Resources Information Center

    Maret, Timothy J.; Ziemba, Robert E.

    1997-01-01

    Suggests that early in their education students be taught to use basic statistical tests as rigorous methods of comparing experimental results with scientific hypotheses. Stresses that students learn how to use statistical tests in hypothesis-testing by applying them in actual hypothesis-testing situations. To illustrate, uses questions such as…

  16. Mesochem: Chemical Dynamics on a Mesoscopic Scale

    SciTech Connect

    Fried, L E; Calef, D F; Wu, C J; Gee, R H

    2004-03-02

    Most chemically stable organic materials age through changes on the mesoscopic scale (from 10 nm to 10 mm). Examples include the slow crystallization of polymers, changes in particle size distributions with age, and the swelling of pressed powders. We began the Mesochem project to develop a new mesoscopic modeling capability for organic materials, including polymers, molecular crystals, and filled polymer composites. Our goal was to develop and validate novel mesoscopic modeling techniques that are well suited for materials of interest to LLNL's nation security mission, such as high explosives, binding agents, and foams.

  17. Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

    ERIC Educational Resources Information Center

    Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

    2015-01-01

    This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

  18. Multidimensional Computerized Adaptive Testing for Indonesia Junior High School Biology

    ERIC Educational Resources Information Center

    Kuo, Bor-Chen; Daud, Muslem; Yang, Chih-Wei

    2015-01-01

    This paper describes a curriculum-based multidimensional computerized adaptive test that was developed for Indonesia junior high school Biology. In adherence to the Indonesian curriculum of different Biology dimensions, 300 items was constructed, and then tested to 2238 students. A multidimensional random coefficients multinomial logit model was…

  19. Mesoscopic Modelling of Financial Markets

    NASA Astrophysics Data System (ADS)

    Cordier, Stephane; Pareschi, Lorenzo; Piatecki, Cyrille

    2009-01-01

    We derive a mesoscopic description of the behavior of a simple financial market where the agents can create their own portfolio between two investment alternatives: a stock and a bond. The model is derived starting from the Levy-Levy-Solomon microscopic model (Levy et al. in Econ. Lett. 45:103-111, 1994; Levy et al. in Microscopic Simulation of Financial Markets: From Investor Behavior to Market Phenomena, Academic Press, San Diego, 2000) using the methods of kinetic theory and consists of a linear Boltzmann equation for the wealth distribution of the agents coupled with an equation for the price of the stock. From this model, under a suitable scaling, we derive a Fokker-Planck equation and show that the equation admits a self-similar lognormal behavior. Several numerical examples are also reported to validate our analysis.

  20. Mesoscopic model for tumor growth.

    PubMed

    Izquierdo-Kulich, Elena; Nieto-Villar, José Manuel

    2007-10-01

    In this work, we propose a mesoscopic model for tumor growth to improve our understanding of the origin of the heterogeneity of tumor cells. In this sense, this stochastic formalism allows us to not only to reproduce but also explain the experimental results presented by Brú. A significant aspect found by the model is related to the predicted values for beta growth exponent, which capture a basic characteristic of the critical surface growth dynamics. According to the model, the value for growth exponent is between 0,25 and 0,5, which includes the value proposed by Kadar-Parisi-Zhang universality class (0,33) and the value proposed by Brú (0,375) related to the molecular beam epitaxy (MBE) universality class. This result suggests that the tumor dynamics are too complex to be associated to a particular universality class.

  1. Nonequilibrium mesoscopic transport: a genealogy.

    PubMed

    Das, Mukunda P; Green, Frederick

    2012-05-09

    Models of nonequilibrium quantum transport underpin all modern electronic devices, from the largest scales to the smallest. Past simplifications such as coarse graining and bulk self-averaging served well to understand electronic materials. Such particular notions become inapplicable at mesoscopic dimensions, edging towards the truly quantum regime. Nevertheless a unifying thread continues to run through transport physics, animating the design of small-scale electronic technology: microscopic conservation and nonequilibrium dissipation. These fundamentals are inherent in quantum transport and gain even greater and more explicit experimental meaning in the passage to atomic-sized devices. We review their genesis, their theoretical context, and their governing role in the electronic response of meso- and nanoscopic systems.

  2. Comparison of agriculture biology and general biology testing outcomes in Utah

    NASA Astrophysics Data System (ADS)

    Despain, Deric Walter

    Agriculture education can take scientific topics to higher levels, emphasize scientific concepts, involve hands-on learning, and develop interrelationships with the other sciences, thus making the living and non-living world around them relevant for students. Prior to 1996, agriculture education was not considered adequate to prepare Utah high school students to meet state biology requirements. The appropriateness of making that equalizing decision in 1996 was not tested until this 2014 study, comparing student test scores on the state biology test for general biology and agriculture biology students. The 2008-2012 data were collected from the Utah Department of Education Data and Statistics, utilizing a descriptive comparative post-test only analysis. As seen in this study, not only did B/AS students tend to score lower than their General Biology counterparts, in multiple cases this difference was significant (p ≤ .05). This contrary finding challenges the theoretical foundation of this study. As a result of this study three implications were made; (a) the Utah CRT-Biology test is not a reliable gauge of academic achievement in agriculture biology, (b) agriculture students in the sample population have not been taught with rigorous biology standards, and (c) biology standards taught in agricultural biology classes are not aligned with content tested by the biology portion of the Utah CRT-Biology test standards. The results of this study indicate to stakeholders that there is a gap occurring within the B/AS education, and the need to reevaluate the biology curriculum delivery to its population may possibly be in need of immediate action.

  3. Hybrid Metallic Mesoscopic Structures:. Some Unanswered Questions

    NASA Astrophysics Data System (ADS)

    Petrashov, V. T.

    2003-03-01

    A brief overview is given of several effects observed experimentally in hybrid metallic nanostructures that require further theoretical analysis and understanding of physics behind them. Those include strong enhancement of the Altshuler-Aronov-Spivak oscillations in normal metallic mesoscopic rings with semi-metallic electrodes, h/4e oscillations in normal mesoscopic rings with interfaces to superconductors (Andreev interferometers), phase flip in the superconducting-phase-periodic oscillations with negative magnetoresistance at low quasiparticle energies in Andreev interferometers.

  4. Drug Development Against Viral Diseases (Biological Testing)

    DTIC Science & Technology

    1992-02-01

    any. sip of infection or disese (11. Also, laboratory work with CCHF has beeni limited because accidental infections which have had serious or even fata...were unldrgoir. i,,¢rois. No leb’ons were found in submaxillary or sublingual salivary gland, kidney , heart, eye, lacrimal gland, thyroid, trachea, or...examined including kidney , lung, liver and brain. e. Active chemotherapeutic agents in the vaccinia tail lesion model. Most drugs tested in thit model gave

  5. Metastable Mesoscopic Phases in Concentrated Protein Solutions

    NASA Astrophysics Data System (ADS)

    Vekilov, P. G.; Pan, W.; Gliko, O.; Katsonis, P.; Galkin, O.

    It is sometimes claimed that the cytosol around the organelles, tubules, and other cellular structures represents a liquid phase. On the other hand, almost all protein molecules in the cytosol participate in complexes with other proteins, nucleic acids, small molecules, etc. The two pictures of a homogeneous liquid and a granular multiscale mixture appear incompatible. Thus, an important question in physical biology is whether the protein complexes represent a property of the protein solutions, or are the result of complex specific interaction involving multiple biological molecules. We apply light scattering, atomic force microscopy, and other techniques to demonstrate that even solutions of a single protein of moderate concentration do not comply with Gibbs's definition of phase. In such solutions clusters of sizes from several tens to several hundred nanometers exist and have limited lifetimes. These clusters have a higher free energy than the protein solution, and their lifetime is determined by a barrier for their decay. The clusters affect the viscous and visco-elastic behavior of the solution and are an essential part of potential condensation and aggregation pathways. Since the clusters are observed in solutions of single proteins, they indicate that the proteins have an intrinsic propensity to form mesoscopic structures, which likely is utilized in the formation of the protein complexes in the cytosol. Cluster theories developed for colloid systems appear inapplicable to proteins due to the high level of implied Coulombic repulsion. A Monte Carlo model with protein-like potentials reproduces the metastable clusters of dense liquid with limited lifetimes and variable sizes, and suggests that the clusters' sizes are determined by the kinetics of growth and decay, and not by thermodynamics. A microscopic theory, which should account for stabilizing and destabilizing factors involving protein molecules and solvent inside the clusters, is still to be developed.

  6. Seismological Field Observation of Mesoscopic Nonlinearity

    NASA Astrophysics Data System (ADS)

    Sens-Schönfelder, Christoph; Gassenmeier, Martina; Eulenfeld, Tom; Tilmann, Frederik; Korn, Michael; Niederleithinger, Ernst

    2016-04-01

    Noise based observations of seismic velocity changes have been made in various environments. We know of seasonal changes of velocities related to ground water or temperature changes, co-seismic changes originating from shaking or stress redistribution and changes related to volcanic activity. Is is often argued that a decrease of velocity is related to the opening of cracks while the closure of cracks leads to a velocity increase if permanent stress changes are invoked. In contrast shaking induced changes are often related to "damage" and subsequent "healing" of the material. The co-seismic decrease and transient recovery of seismic velocities can thus be explained with both - static stress changes or damage/healing processes. This results in ambiguous interpretations of the observations. Here we present the analysis of one particular seismic station in northern Chile that shows very strong and clear velocity changes associated with several earthquakes ranging from Mw=5.3 to Mw=8.1. The fact that we can observe the response to several events of various magnitudes from different directions offers the unique possibility to discern the two possible causative processes. We test the hypothesis, that the velocity changes are related to shaking rather than stress changes by developing an empirical model that is based on the local ground acceleration at the sensor site. The eight year of almost continuous observations of velocity changes are well modeled by a daily drop of the velocity followed by an exponential recovery. Both, the amplitude of the drop as well as the recovery time are proportional to the integrated acceleration at the seismic station. Effects of consecutive days are independent and superimposed resulting in strong changes after earthquakes and constantly increasing velocities during quiet days thereafter. This model describes the continuous observations of the velocity changes solely based on the acceleration time series without individually defined dates

  7. Using synthetic biology to make cells tomorrow's test tubes.

    PubMed

    Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

    2016-04-18

    The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

  8. Mesoscopic model of actin-based propulsion.

    PubMed

    Zhu, Jie; Mogilner, Alex

    2012-01-01

    Two theoretical models dominate current understanding of actin-based propulsion: microscopic polymerization ratchet model predicts that growing and writhing actin filaments generate forces and movements, while macroscopic elastic propulsion model suggests that deformation and stress of growing actin gel are responsible for the propulsion. We examine both experimentally and computationally the 2D movement of ellipsoidal beads propelled by actin tails and show that neither of the two models can explain the observed bistability of the orientation of the beads. To explain the data, we develop a 2D hybrid mesoscopic model by reconciling these two models such that individual actin filaments undergoing nucleation, elongation, attachment, detachment and capping are embedded into the boundary of a node-spring viscoelastic network representing the macroscopic actin gel. Stochastic simulations of this 'in silico' actin network show that the combined effects of the macroscopic elastic deformation and microscopic ratchets can explain the observed bistable orientation of the actin-propelled ellipsoidal beads. To test the theory further, we analyze observed distribution of the curvatures of the trajectories and show that the hybrid model's predictions fit the data. Finally, we demonstrate that the model can explain both concave-up and concave-down force-velocity relations for growing actin networks depending on the characteristic time scale and network recoil. To summarize, we propose that both microscopic polymerization ratchets and macroscopic stresses of the deformable actin network are responsible for the force and movement generation.

  9. Mesoscopic Model of Actin-Based Propulsion

    PubMed Central

    Zhu, Jie; Mogilner, Alex

    2012-01-01

    Two theoretical models dominate current understanding of actin-based propulsion: microscopic polymerization ratchet model predicts that growing and writhing actin filaments generate forces and movements, while macroscopic elastic propulsion model suggests that deformation and stress of growing actin gel are responsible for the propulsion. We examine both experimentally and computationally the 2D movement of ellipsoidal beads propelled by actin tails and show that neither of the two models can explain the observed bistability of the orientation of the beads. To explain the data, we develop a 2D hybrid mesoscopic model by reconciling these two models such that individual actin filaments undergoing nucleation, elongation, attachment, detachment and capping are embedded into the boundary of a node-spring viscoelastic network representing the macroscopic actin gel. Stochastic simulations of this ‘in silico’ actin network show that the combined effects of the macroscopic elastic deformation and microscopic ratchets can explain the observed bistable orientation of the actin-propelled ellipsoidal beads. To test the theory further, we analyze observed distribution of the curvatures of the trajectories and show that the hybrid model's predictions fit the data. Finally, we demonstrate that the model can explain both concave-up and concave-down force-velocity relations for growing actin networks depending on the characteristic time scale and network recoil. To summarize, we propose that both microscopic polymerization ratchets and macroscopic stresses of the deformable actin network are responsible for the force and movement generation. PMID:23133366

  10. Resource Letter: MesP-1: Mesoscopic physics

    NASA Astrophysics Data System (ADS)

    Glazman, L. I.

    2002-04-01

    This Resource Letter provides a guide to the literature on mesoscopic electron physics of solids. Journal articles, conference proceedings, and books are cited for the following topics: conductance fluctuations in disordered and quantum-chaotic systems, conductance quantization, conduction of a Luttinger liquid, electron noise in mesoscopic devices, mesoscopic superconductivity, electron-electron interactions in mesoscopic systems and the Coulomb blockade phenomenon, and Kondo effect in quantum dots.

  11. UNDERSTANDINGS OF BSCS BIOLOGY STUDENTS AS DETERMINED BY INSTRUCTIONAL TESTS.

    ERIC Educational Resources Information Center

    ROBINSON, JAMES T.

    EIGHT INSTRUCTIONAL TESTS SPANNED THE CURRICULUM OF ONE YEAR OF BIOLOGY STUDY. THE FIRST CONCERNED THE NATURE OF SCIENCE INCLUDED 4 AREAS OF EMPHASIS--THE NATURE AND FUNCTION OF HYPOTHESIS, THE IDEA OF CONTROLS IN EXPERIMENTS, INTERPRETATION OF GRAPHED DATA, AND THE NATURE OF DATA. THE SECOND TEST WAS DESIGNED TO SHOW AN UNDERSTANDING OF…

  12. UNDERSTANDINGS OF BSCS BIOLOGY STUDENTS AS DETERMINED BY INSTRUCTIONAL TESTS.

    ERIC Educational Resources Information Center

    ROBINSON, JAMES T.

    EIGHT INSTRUCTIONAL TESTS SPANNED THE CURRICULUM OF ONE YEAR OF BIOLOGY STUDY. THE FIRST CONCERNED THE NATURE OF SCIENCE INCLUDED 4 AREAS OF EMPHASIS--THE NATURE AND FUNCTION OF HYPOTHESIS, THE IDEA OF CONTROLS IN EXPERIMENTS, INTERPRETATION OF GRAPHED DATA, AND THE NATURE OF DATA. THE SECOND TEST WAS DESIGNED TO SHOW AN UNDERSTANDING OF…

  13. Mesoscopic Modeling of Reactive Transport Processes

    NASA Astrophysics Data System (ADS)

    Kang, Q.; Chen, L.; Deng, H.

    2012-12-01

    Reactive transport processes involving precipitation and/or dissolution are pervasive in geochemical, biological and engineered systems. Typical examples include self-assembled patterns such as Liesegang rings or bands, cones of stalactites in limestones caves, biofilm growth in aqueous environment, formation of mineral deposits in boilers and heat exchangers, uptake of toxic metal ions from polluted water by calcium carbonate, and mineral trapping of CO2. Compared to experimental studies, a numerical approach enables a systematic study of the reaction kinetics, mass transport, and mechanisms of nucleation and crystal growth, and hence provides a detailed description of reactive transport processes. In this study, we enhance a previously developed lattice Boltzmann pore-scale model by taking into account the nucleation process, and develop a mesoscopic approach to simulate reactive transport processes involving precipitation and/or dissolution of solid phases. The model is then used to simulate the formation of Liesegang precipitation patterns and investigate the effects of gel on the morphology of the precipitates. It is shown that this model can capture the porous structures of the precipitates and can account for the effects of the gel concentration and material. A wide range of precipitation patterns is predicted under different gel concentrations, including regular bands, treelike patterns, and for the first time with numerical models, transition patterns from regular bands to treelike patterns. The model is also applied to study the effect of secondary precipitate on the dissolution of primary mineral. Several types of dissolution and precipitation processes are identified based on the morphology and structures of the precipitates and on the extent to which the precipitates affect the dissolution of the primary mineral. Finally the model is applied to study the formation of pseudomorph. It is demonstrated for the first time by numerical simulation that a

  14. Revealing mesoscopic structural universality with diffusion.

    PubMed

    Novikov, Dmitry S; Jensen, Jens H; Helpern, Joseph A; Fieremans, Els

    2014-04-08

    Measuring molecular diffusion is widely used for characterizing materials and living organisms noninvasively. This characterization relies on relations between macroscopic diffusion metrics and structure at the mesoscopic scale commensurate with the diffusion length. Establishing such relations remains a fundamental challenge, hindering progress in materials science, porous media, and biomedical imaging. Here we show that the dynamical exponent in the time dependence of the diffusion coefficient distinguishes between the universality classes of the mesoscopic structural complexity. Our approach enables the interpretation of diffusion measurements by objectively selecting and modeling the most relevant structural features. As an example, the specific values of the dynamical exponent allow us to identify the relevant mesoscopic structure affecting MRI-measured water diffusion in muscles and in brain, and to elucidate the structural changes behind the decrease of diffusion coefficient in ischemic stroke.

  15. Persistent currents in mesoscopic Fibonacci rings

    SciTech Connect

    Jin, G.J.; Wang, Z.D.; Hu, A.; Jiang, S.S.

    1997-04-01

    In the framework of a tight-binding model, we study energy spectra and persistent currents in mesoscopic Fibonacci rings threaded by a magnetic flux. It is found that the flux-dependent electron eigenenergies E({Phi}) in mesoscopic Fibonacci rings still form ``bands`` with respect to the flux {Phi}, but there is a scaling relation between the total ``bandwidth`` and the Fibonacci number. When the strength of the one-dimensional quasiperiodic potential increases, the persistent current decreases rapidly. Interestingly, for a generalized mixing model of mesoscopic Fibonacci rings, free-electron-like persistent current may appear if the number of electrons of the system takes a specific value. {copyright} {ital 1997} {ital The American Physical Society}

  16. Suppression of superconductivity in mesoscopic superconductors.

    PubMed

    Sobnack, M B; Kusmartsev, F V

    2001-01-22

    We propose a new boundary-driven phase transition associated with vortex nucleation in mesoscopic superconductors (of size of the order of, or larger than, the penetration depth). We derive the rescaling equations and we show that boundary effects associated with vortex nucleation lower the conventional transition temperature in mesoscopic superconductors by an amount which is a function of the size of the superconductor. This result explains recent experiments in small superconductors where it was found that the transition temperature depends on the size of the system and is lower than the critical Berezinskĭ-Kosterlitz-Thouless temperature.

  17. Accurate atom counting in mesoscopic ensembles.

    PubMed

    Hume, D B; Stroescu, I; Joos, M; Muessel, W; Strobel, H; Oberthaler, M K

    2013-12-20

    Many cold atom experiments rely on precise atom number detection, especially in the context of quantum-enhanced metrology where effects at the single particle level are important. Here, we investigate the limits of atom number counting via resonant fluorescence detection for mesoscopic samples of trapped atoms. We characterize the precision of these fluorescence measurements beginning from the single-atom level up to more than one thousand. By investigating the primary noise sources, we obtain single-atom resolution for atom numbers as high as 1200. This capability is an essential prerequisite for future experiments with highly entangled states of mesoscopic atomic ensembles.

  18. Accurate Atom Counting in Mesoscopic Ensembles

    NASA Astrophysics Data System (ADS)

    Hume, D. B.; Stroescu, I.; Joos, M.; Muessel, W.; Strobel, H.; Oberthaler, M. K.

    2013-12-01

    Many cold atom experiments rely on precise atom number detection, especially in the context of quantum-enhanced metrology where effects at the single particle level are important. Here, we investigate the limits of atom number counting via resonant fluorescence detection for mesoscopic samples of trapped atoms. We characterize the precision of these fluorescence measurements beginning from the single-atom level up to more than one thousand. By investigating the primary noise sources, we obtain single-atom resolution for atom numbers as high as 1200. This capability is an essential prerequisite for future experiments with highly entangled states of mesoscopic atomic ensembles.

  19. Current challenges and opportunities in nonclinical safety testing of biologics.

    PubMed

    Kronenberg, Sven; Baumann, Andreas; de Haan, Lolke; Hinton, Heather J; Moggs, Jonathan; Theil, Frank-Peter; Wakefield, Ian; Singer, Thomas

    2013-12-01

    Nonclinical safety testing of new biotherapeutic entities represents its own challenges and opportunities in drug development. Hot topics in this field have been discussed recently at the 2nd Annual BioSafe European General Membership Meeting. In this feature article, discussions on the challenges surrounding the use of PEGylated therapeutic proteins, selection of cynomolgus monkey as preclinical species, unexpected pharmacokinetics of biologics and the safety implications thereof are summarized. In addition, new developments in immunosafety testing of biologics, the use of transgenic mouse models and PK and safety implications of multispecific targeting approaches are discussed. Overall, the increasing complexity of new biologic modalities and formats warrants tailor-made nonclinical development strategies and experimental testing.

  20. What can we learn from noise? — Mesoscopic nonequilibrium statistical physics —

    PubMed Central

    KOBAYASHI, Kensuke

    2016-01-01

    Mesoscopic systems — small electric circuits working in quantum regime — offer us a unique experimental stage to explorer quantum transport in a tunable and precise way. The purpose of this Review is to show how they can contribute to statistical physics. We introduce the significance of fluctuation, or equivalently noise, as noise measurement enables us to address the fundamental aspects of a physical system. The significance of the fluctuation theorem (FT) in statistical physics is noted. We explain what information can be deduced from the current noise measurement in mesoscopic systems. As an important application of the noise measurement to statistical physics, we describe our experimental work on the current and current noise in an electron interferometer, which is the first experimental test of FT in quantum regime. Our attempt will shed new light in the research field of mesoscopic quantum statistical physics. PMID:27477456

  1. A living mesoscopic cellular automaton made of skin scales

    NASA Astrophysics Data System (ADS)

    Manukyan, Liana; Montandon, Sophie A.; Fofonjka, Anamarija; Smirnov, Stanislav; Milinkovitch, Michel C.

    2017-04-01

    In vertebrates, skin colour patterns emerge from nonlinear dynamical microscopic systems of cell interactions. Here we show that in ocellated lizards a quasi-hexagonal lattice of skin scales, rather than individual chromatophore cells, establishes a green and black labyrinthine pattern of skin colour. We analysed time series of lizard scale colour dynamics over four years of their development and demonstrate that this pattern is produced by a cellular automaton (a grid of elements whose states are iterated according to a set of rules based on the states of neighbouring elements) that dynamically computes the colour states of individual mesoscopic skin scales to produce the corresponding macroscopic colour pattern. Using numerical simulations and mathematical derivation, we identify how a discrete von Neumann cellular automaton emerges from a continuous Turing reaction-diffusion system. Skin thickness variation generated by three-dimensional morphogenesis of skin scales causes the underlying reaction-diffusion dynamics to separate into microscopic and mesoscopic spatial scales, the latter generating a cellular automaton. Our study indicates that cellular automata are not merely abstract computational systems, but can directly correspond to processes generated by biological evolution.

  2. Stationary Flux in Mesoscopic Noisy Cylinders

    NASA Astrophysics Data System (ADS)

    Dajka, J.; Łuczka, J.; Szopa, M.

    2003-07-01

    The aim of this paper is to investigate the existence of the stationary states of current in the mesoscopic cylinder. The dynamics of the flux is governed by a stochastic differential equation. We discuss both the influence of equilibrium (thermal) and non-equilibrium noise sources.

  3. Mesoscopic Rings with Spin-Orbit Interactions

    ERIC Educational Resources Information Center

    Berche, Bertrand; Chatelain, Christophe; Medina, Ernesto

    2010-01-01

    A didactic description of charge and spin equilibrium currents on mesoscopic rings in the presence of spin-orbit interaction is presented. Emphasis is made on the non-trivial construction of the correct Hamiltonian in polar coordinates, the calculation of eigenvalues and eigenfunctions and the symmetries of the ground-state properties. Spin…

  4. Mesoscopic Rings with Spin-Orbit Interactions

    ERIC Educational Resources Information Center

    Berche, Bertrand; Chatelain, Christophe; Medina, Ernesto

    2010-01-01

    A didactic description of charge and spin equilibrium currents on mesoscopic rings in the presence of spin-orbit interaction is presented. Emphasis is made on the non-trivial construction of the correct Hamiltonian in polar coordinates, the calculation of eigenvalues and eigenfunctions and the symmetries of the ground-state properties. Spin…

  5. - and Mesoscopic Patterns on Semiconductor Surfaces

    NASA Astrophysics Data System (ADS)

    Samuilov, Vladimir; Seo, Young-Soo; Ksenevich, Vitaly; Galibert, Jean; Sokolov, Jonathan; Rafailovich, Miriam

    2002-03-01

    A novel and simple approach of self-organized fabrication of two dimensional mesoscopic networks with the feature size down to 50 nm has been developed. The technique is based on the self-organized patterning in a thin layer of complex liquid (polymer solution) in the presence of humid atmosphere. Two dimensional mesoscopic honeycomb-shaped carbon structures were produced by high temperature annealing of nitrocellulose precursors [1]. The polymer network was also utilized as a mask for further reactive ion etching of surfaces with epi-layer of GaAs [2,3] and GaAs/AlGaAs d -doped heterostructures [4]. These structures can be considered as regular arrays of mesoscopic cells or 2-D photonic band gap crystals. Also, we have used diblock-copolymer system, self-assembled with L-B technique, to produce nano-patterns. These structures were utilized as templates for introducing metal nanopatterns on semiconductor surfaces by reactive ion beam etching for magnetic storage systems [5] and DNA separation on a flat surface [6] devices. 1. V.A. Samuilov, J. Galibert, V.K. Ksenevich, V.J. Goldman, M. Rafailovich, J. Sokolov, I.A. Bashmakov, V.A. Dorosinets, Magnetotransport in mesoscopic carbon networks, Physica B, 294-295, p.p.319-323, 2001. 2. V.A. Samuilov, I.B. Butylina, L.V. Govor, V.K. Ksenevich, I.A. Bashmakov, I.M. Grigorieva, L.V. Solovjova, Fabrication of regular mesoscopic networks of GaAs wires, Superlattices and Microstructures, 25: (1-2) p.p.127-130, 1999. 3. V.A. Samuilov, I.B. Butylina, V.K. Ksenevich, G. Kiss, G. Remenyi, Observation of transport in mesoscopic honeycomb-shaped networks, Superlattices and Microstructures, 25: (1-2) p.p.197-202, 1999 4. J. Galibert, V.A. Samuilov, V.K. Ksenevich, M. Rafailovich, J. Sokolov, Magnetoresistance of low dimensional mesoscopic honeycomb-shape GaAs networks, Physica B, 294-295, p.p.314-318, 2001. 5. S. Zhu, R.J. Gambino, M.H. Rafailovich, J. Sokolov, S.A. Schwarz, and R.D. Gomez, "Microscopic Magnetic Characterization of

  6. Pulse Duplicator Hydrodynamic Testing of Bioengineered Biological Heart Valves.

    PubMed

    Buse, Eric E; Hilbert, Stephen L; Hopkins, Richard A; Converse, Gabriel L

    2016-12-01

    There are many heart valve replacements currently available on the market; however, these devices are not ideal for pediatric patients with congenital heart valve defects. Decellularized valve substitutes offer potential for improved clinical outcomes and require pre-clinical testing guidelines and testing systems suitable for non-crosslinked, biological heart valves. The objective of this study was to assess the hydrodynamic performance of intact, bioengineered pulmonary valves using a custom pulse duplicator capable of testing intact biological valved conduits. The mechanical behavior of valve associated sinus and arterial tissue was also evaluated under biaxial loading. Cryopreserved, decellularized, extracellular matrix (ECM) conditioned and glutaraldehyde fixed valves showed reduced pressure gradients and increased effective orifice area for decellularized and ECM conditioned valves. ECM conditioning resulted in increased elastic modulus but decreased stretch in circumferential and longitudinal directions under biaxial loading. Overall, decellularization and ECM conditioning did not compromise the scaffolds, which exhibited satisfactory bench top performance.

  7. A new biological test of water toxicity-yeast Saccharomyces cerevisiae conductometric test.

    PubMed

    Dolezalova, Jaroslava; Rumlova, Lubomira

    2014-11-01

    This new biological test of water toxicity is based on monitoring of specific conductivity changes of yeast Saccharomyces cerevisiae suspension as a result of yeast fermentation activity inhibition in toxic conditions. The test was verified on ten substances with various mechanisms of toxic effect and the results were compared with two standard toxicity tests based on Daphnia magna mobility inhibition (EN ISO 6341) and Vibrio fischeri bioluminescence inhibition (EN ISO 11348-2) and with the results of the S. cerevisiae lethal test (Rumlova and Dolezalova, 2012). The new biological test - S. cerevisiae conductometric test - is an express method developed primarily for field conditions. It is applicable in case of need of immediate information about water toxicity. Fast completion is an advantage of this test (time necessary for test completion is about 60min), the test is simple and the test organism - dried instant yeast - belongs among its biggest advantages because of its long-term storage life and broad availability.

  8. Testing of Synthetic Biological Membranes for Forward Osmosis Applications

    NASA Technical Reports Server (NTRS)

    Parodi, Jurek; Mangado, Jaione Romero; Stefanson, Ofir; Flynn, Michael; Mancinelli, Rocco; Kawashima, Brian; Trieu, Serena; Brozell, Adrian; Rosenberg, Kevan

    2016-01-01

    Commercially available forward osmosis membranes have been extensively tested for human space flight wastewater treatment. Despite the improvements achieved in the last decades, there is still a challenge to produce reliable membranes with anti-fouling properties, chemical resistance, and high flux and selectivity. Synthetic biological membranes that mimic the ones present in nature, which underwent millions of years of evolution, represent a potential solution for further development and progress in membrane technology. Biomimetic forward osmosis membranes based on a polymeric support filter and coated with surfactant multilayers have been engineered to investigate how different manufacturing processes impact the performance and structure of the membrane. However, initial results of the first generation prototype membranes tests reveal a high scatter in the data, due to the current testing apparatus set up. The testing apparatus has been upgraded to improve data collection, reduce errors, and to allow higher control of the testing process.

  9. Biological testing of a digested sewage sludge and derived composts.

    PubMed

    Moreira, R; Sousa, J P; Canhoto, C

    2008-11-01

    Aiming to evaluate a possible loss of soil habitat function after amendment with organic wastes, a digested sewage sludge and derived composts produced with green residues, where biologically tested in the laboratory using soil animals (Eisenia andrei and Folsomia candida) and plants (Brassica rapa and Avena sativa). Each waste was tested mimicking a field application of 6ton/ha or 12ton/ha. Avoidance tests did not reveal any impact of sludge and composts to soil biota. Germination and growth tests showed that application of composts were beneficial for both plants. Composts did not affect earthworm's mass increase or reproduction, but the highest sludge amendment revealed negative effects on both parameters. Only the amendment of composts at the highest dose originated an impairment of springtails reproductive output. We suggest that bioassays using different test species may be an additional tool to evaluate effects of amendment of organic wastes in soil. Biological tests are sensitive to pollutants at low concentrations and to interactions undetected by routine chemical analysis.

  10. Wave basin model tests of technical-biological bank protection

    NASA Astrophysics Data System (ADS)

    Eisenmann, J.

    2012-04-01

    Sloped embankments of inland waterways are usually protected from erosion and other negative im-pacts of ship-induced hydraulic loads by technical revetments consisting of riprap. Concerning the dimensioning of such bank protection there are several design rules available, e.g. the "Principles for the Design of Bank and Bottom Protection for Inland Waterways" or the Code of Practice "Use of Standard Construction Methods for Bank and Bottom Protection on Waterways" issued by the BAW (Federal Waterways Engineering and Research Institute). Since the European Water Framework Directive has been put into action special emphasis was put on natural banks. Therefore the application of technical-biological bank protection is favoured. Currently design principles for technical-biological bank protection on inland waterways are missing. The existing experiences mainly refer to flowing waters with no or low ship-induced hydraulic loads on the banks. Since 2004 the Federal Waterways Engineering and Research Institute has been tracking the re-search and development project "Alternative Technical-Biological Bank Protection on Inland Water-ways" in company with the Federal Institute of Hydrology. The investigation to date includes the ex-amination of waterway sections where technical- biological bank protection is applied locally. For the development of design rules for technical-biological bank protection investigations shall be carried out in a next step, considering the mechanics and resilience of technical-biological bank protection with special attention to ship-induced hydraulic loads. The presentation gives a short introduction into hydraulic loads at inland waterways and their bank protection. More in detail model tests of a willow brush mattress as a technical-biological bank protec-tion in a wave basin are explained. Within the scope of these tests the brush mattresses were ex-posed to wave impacts to determine their resilience towards hydraulic loads. Since the

  11. Mesoscopic Structure Conditions the Emergence of Cooperation on Social Networks

    PubMed Central

    Lozano, Sergi; Arenas, Alex; Sánchez, Angel

    2008-01-01

    Background We study the evolutionary Prisoner's Dilemma on two social networks substrates obtained from actual relational data. Methodology/Principal Findings We find very different cooperation levels on each of them that cannot be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifically designed artificial networks, finding a good agreement with the observations in both real substrates. Conclusion Our results support the conclusion that studies of evolutionary games on model networks and their interpretation in terms of global properties may not be sufficient to study specific, real social systems. Further, the study allows us to define new quantitative parameters that summarize the mesoscopic structure of any network. In addition, the community perspective may be helpful to interpret the origin and behavior of existing networks as well as to design structures that show resilient cooperative behavior. PMID:18382673

  12. Mesoscopic structure conditions the emergence of cooperation on social networks

    SciTech Connect

    Lozano, S.; Arenas, A.; Sanchez, A.

    2008-12-01

    We study the evolutionary Prisoner's Dilemma on two social networks substrates obtained from actual relational data. We find very different cooperation levels on each of them that cannot be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifically designed artificial networks, finding a good agreement with the observations in both real substrates. Our results support the conclusion that studies of evolutionary games on model networks and their interpretation in terms of global properties may not be sufficient to study specific, real social systems. Further, the study allows us to define new quantitative parameters that summarize the mesoscopic structure of any network. In addition, the community perspective may be helpful to interpret the origin and behavior of existing networks as well as to design structures that show resilient cooperative behavior.

  13. A NONLINEAR MESOSCOPIC ELASTIC CLASS OF MATERIALS

    SciTech Connect

    P. JOHNSON; R. GUYER; L. OSTROVSKY

    1999-09-01

    It is becoming clear that the elastic properties of rock are shared by numerous other materials (sand, soil, some ceramics, concrete, etc.). These materials have one or more of the following properties in common strong nonlinearity, hysteresis in stress-strain relation, slow dynamics and discrete memory. Primarily, it is the material's compliance, the mesoscopic linkages between the rigid components, that give these materials their unusual elastic properties.

  14. Secure communication using mesoscopic coherent states.

    PubMed

    Barbosa, Geraldo A; Corndorf, Eric; Kumar, Prem; Yuen, Horace P

    2003-06-06

    We demonstrate theoretically and experimentally that secure communication using intermediate-energy (mesoscopic) coherent states is possible. Our scheme is different from previous quantum cryptographic schemes in that a short secret key is explicitly used and in which quantum noise hides both the bit and the key. This encryption scheme allows optical amplification. New avenues are open to secure communications at high speeds in fiber-optic or free-space channels.

  15. Mesoscopic physics and nanoelectronics: nanoscience and nanotechnology

    NASA Astrophysics Data System (ADS)

    Buot, Felix A.

    1993-11-01

    A coherent overview of the exciting field and challenging areas of research in mesoscopic physics and nanoelectronics is given. The unifying role of the S-matrix theory or “ input-quantum process-output” language of quantum mechanics in the formulation of quantum transport in mesoscopic physics and nanoelectronics is clarified, with time-independent S-matrix theory applied to mesoscopic systems and double-time-axis time-dependent S-matrix thoory, coupled with the lattice Weyl-Wigner formulation of quantum dynamics of electrons in solids, applied to the highly nonlinear, far-from-equilibrium and high-speed nanoelectronic devices. At steady state and near equilibrium, the two independent formulations yield equivalent results. The technological impact of the many-body quantum distribution-function (QDF) (typified by the Wigner distribution function) approach is demonstrated by a complete transition from the level of basic nonlinear quantum transport physics to an engineering computer-aided design tool for integrated circuits (ICs). This is done in the derivation of the equivalent circuit model for resonant tunneling devices which incorporates the quantum inductance. In this review, emphasis is given to major developments in quantum transport, computational nanoelectronics, new device concepts, and novel transport physical phenomena found in small structures, with potential device and IC applications and deemed most likely to have a significant impact on the future developments of nanoelectronics.

  16. Entropy production in mesoscopic stochastic thermodynamics: nonequilibrium kinetic cycles driven by chemical potentials, temperatures, and mechanical forces.

    PubMed

    Qian, Hong; Kjelstrup, Signe; Kolomeisky, Anatoly B; Bedeaux, Dick

    2016-04-20

    Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport, diffusion, thermochemical, thermomechanical and mechanochemical fluxes. In the present review, we introduce a mesoscopic stochastic formulation of NET by analyzing entropy production in several simple examples. The fundamental role of nonequilibrium steady-state cycle kinetics is emphasized. The statistical mechanics of Onsager's reciprocal relations in this context is elucidated. Chemomechanical, thermomechanical, and enzyme-catalyzed thermochemical energy transduction processes are discussed. It is argued that mesoscopic stochastic NET in phase space provides a rigorous mathematical basis of fundamental concepts needed for understanding complex processes in chemistry, physics and biology. This theory is also relevant for nanoscale technological advances.

  17. Entropy production in mesoscopic stochastic thermodynamics: nonequilibrium kinetic cycles driven by chemical potentials, temperatures, and mechanical forces

    NASA Astrophysics Data System (ADS)

    Qian, Hong; Kjelstrup, Signe; Kolomeisky, Anatoly B.; Bedeaux, Dick

    2016-04-01

    Nonequilibrium thermodynamics (NET) investigates processes in systems out of global equilibrium. On a mesoscopic level, it provides a statistical dynamic description of various complex phenomena such as chemical reactions, ion transport, diffusion, thermochemical, thermomechanical and mechanochemical fluxes. In the present review, we introduce a mesoscopic stochastic formulation of NET by analyzing entropy production in several simple examples. The fundamental role of nonequilibrium steady-state cycle kinetics is emphasized. The statistical mechanics of Onsager’s reciprocal relations in this context is elucidated. Chemomechanical, thermomechanical, and enzyme-catalyzed thermochemical energy transduction processes are discussed. It is argued that mesoscopic stochastic NET in phase space provides a rigorous mathematical basis of fundamental concepts needed for understanding complex processes in chemistry, physics and biology. This theory is also relevant for nanoscale technological advances.

  18. Nondestructive mechanical characterization of developing biological tissues using inflation testing.

    PubMed

    Oomen, P J A; van Kelle, M A J; Oomens, C W J; Bouten, C V C; Loerakker, S

    2017-10-01

    One of the hallmarks of biological soft tissues is their capacity to grow and remodel in response to changes in their environment. Although it is well-accepted that these processes occur at least partly to maintain a mechanical homeostasis, it remains unclear which mechanical constituent(s) determine(s) mechanical homeostasis. In the current study a nondestructive mechanical test and a two-step inverse analysis method were developed and validated to nondestructively estimate the mechanical properties of biological tissue during tissue culture. Nondestructive mechanical testing was achieved by performing an inflation test on tissues that were cultured inside a bioreactor, while the tissue displacement and thickness were nondestructively measured using ultrasound. The material parameters were estimated by an inverse finite element scheme, which was preceded by an analytical estimation step to rapidly obtain an initial estimate that already approximated the final solution. The efficiency and accuracy of the two-step inverse method was demonstrated on virtual experiments of several material types with known parameters. PDMS samples were used to demonstrate the method's feasibility, where it was shown that the proposed method yielded similar results to tensile testing. Finally, the method was applied to estimate the material properties of tissue-engineered constructs. Via this method, the evolution of mechanical properties during tissue growth and remodeling can now be monitored in a well-controlled system. The outcomes can be used to determine various mechanical constituents and to assess their contribution to mechanical homeostasis. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Biological Aerosol Test Method and Personal Protective Equipment (PPE) Decon

    DTIC Science & Technology

    2011-05-01

    time they were used for viral TCID50 assay(s). The Spearman – Karber formula (Appendix C, C-3) was used to determine the concentration of viable virus...300 mL 50% glutaraldehyde, 2700 mL H2O. E-3 Virus quantification Spearman – Karber formula L = log10 TCID50 titer = X0 - (d/2) + d *∑ri/ni...AFRL-RX-TY-TR-2010-0070 BIOLOGICAL AEROSOL TEST METHOD AND PERSONAL PROTECTIVE EQUIPMENT (PPE) DECON Steven H. Hinrichs, Michael B

  20. A drop tower for controlled impact testing of biological tissues.

    PubMed

    Burgin, Leanne V; Aspden, Richard M

    2007-05-01

    Impact damage, in particular to tissues such as articular cartilage, is a recognised source of morbidity. To understand better the clinical outcomes, it is important to know the mechanics of the damage sustained and the biological response of cells to rapidly applied forces and subsequent tissue disruption. An instrumented drop tower has been designed to enable controlled impact loads to be applied to small samples of biological materials. Impact severity can be controlled by using impactors of different masses and various drop heights. Force and deceleration at impact are recorded at 50,000 samples s(-1) by a force transducer under the sample and an accelerometer on the impactor. Repeatability was tested on rubber washers and coefficients of variation were found to be better than 8% for dynamic stiffness, 3.4% for stress and 4.3% for strain. Initial tests on isolated biopsies of articular cartilage showed that at an initial strain rate of 916 s(-1), the peak dynamic modulus of human femoral head cartilage was 59 MPa, and for a bovine biopsy the initial strain rate and corresponding peak dynamic modulus were 3380 s(-1) and 130 MPa, respectively. The equipment described is capable of applying an impact load to small biopsies of tissue with a defined energy and velocity and measuring deformation and load at high rates of loading.

  1. Dynamic quantum tunneling in mesoscopic driven Duffing oscillators.

    PubMed

    Guo, Lingzhen; Zheng, Zhigang; Li, Xin-Qi; Yan, Yijing

    2011-07-01

    We investigate the dynamic quantum tunneling between two attractors of a mesoscopic driven Duffing oscillator. We find that, in addition to inducing a remarkable quantum shift of the bifurcation point, the mesoscopic nature also results in a perfect linear scaling behavior for the tunneling rate with the driving distance to the shifted bifurcation point.

  2. Current Correlations from a Mesoscopic Anyon Collider.

    PubMed

    Rosenow, Bernd; Levkivskyi, Ivan P; Halperin, Bertrand I

    2016-04-15

    Fermions and bosons are fundamental realizations of exchange statistics, which governs the probability for two particles being close to each other spatially. Anyons in the fractional quantum Hall effect are an example for exchange statistics intermediate between bosons and fermions. We analyze a mesoscopic setup in which two dilute beams of anyons collide with each other, and relate the correlations of current fluctuations to the probability of particles excluding each other spatially. While current correlations for fermions vanish, negative correlations for anyons are a clear signature of a reduced spatial exclusion as compared to fermions.

  3. Quantum measurement of a mesoscopic spin ensemble

    SciTech Connect

    Giedke, G.; Taylor, J. M.; Lukin, M. D.; D'Alessandro, D.; Imamoglu, A.

    2006-09-15

    We describe a method for precise estimation of the polarization of a mesoscopic spin ensemble by using its coupling to a single two-level system. Our approach requires a minimal number of measurements on the two-level system for a given measurement precision. We consider the application of this method to the case of nuclear-spin ensemble defined by a single electron-charged quantum dot: we show that decreasing the electron spin dephasing due to nuclei and increasing the fidelity of nuclear-spin-based quantum memory could be within the reach of present day experiments.

  4. Mesoscopic systems: classical irreversibility and quantum coherence.

    PubMed

    Barbara, Bernard

    2012-09-28

    Mesoscopic physics is a sub-discipline of condensed-matter physics that focuses on the properties of solids in a size range intermediate between bulk matter and individual atoms. In particular, it is characteristic of a domain where a certain number of interacting objects can easily be tuned between classical and quantum regimes, thus enabling studies at the border of the two. In magnetism, such a tuning was first realized with large-spin magnetic molecules called single-molecule magnets (SMMs) with archetype Mn(12)-ac. In general, the mesoscopic scale can be relatively large (e.g. micrometre-sized superconducting circuits), but, in magnetism, it is much smaller and can reach the atomic scale with rare earth (RE) ions. In all cases, it is shown how quantum relaxation can drastically reduce classical irreversibility. Taking the example of mesoscopic spin systems, the origin of irreversibility is discussed on the basis of the Landau-Zener model. A classical counterpart of this model is described enabling, in particular, intuitive understanding of most aspects of quantum spin dynamics. The spin dynamics of mesoscopic spin systems (SMM or RE systems) becomes coherent if they are well isolated. The study of the damping of their Rabi oscillations gives access to most relevant decoherence mechanisms by different environmental baths, including the electromagnetic bath of microwave excitation. This type of decoherence, clearly seen with spin systems, is easily recovered in quantum simulations. It is also observed with other types of qubits such as a single spin in a quantum dot or a superconducting loop, despite the presence of other competitive decoherence mechanisms. As in the molecular magnet V(15), the leading decoherence terms of superconducting qubits seem to be associated with a non-Markovian channel in which short-living entanglements with distributions of two-level systems (nuclear spins, impurity spins and/or charges) leading to 1/f noise induce τ(1)-like

  5. Spatially resolved photonic transfer through mesoscopic heterowires.

    PubMed

    Quidant, R; Weeber, J-C; Dereux, A; Peyrade, D; Girard, Ch; Chen, Y

    2002-03-01

    We report spatially resolved observations of light wave propagation along high refraction index dielectric heterowires lying on a transparent substrate. The heterowires are made of linear chains of closely packed mesoscopic particles. The optical excitation of these heterowires is performed through channel waveguides featuring submicrometer transverse cross sections. Both numerical simulations and near-field optical images, recorded with a photon scanning tunneling microscope, agree to show that, at visible frequencies, tuning the periodicity of the heterowires controls the propagation length within a range of several micrometers.

  6. Mesoscopic admittance of a double quantum dot

    SciTech Connect

    Cottet, Audrey; Mora, Christophe; Kontos, Takis

    2011-03-15

    We calculate the mesoscopic admittance G({omega}) of a double quantum dot (DQD), which can be measured directly using microwave techniques. This quantity reveals spectroscopic information on the DQD and is also directly sensitive to a Pauli spin blockade effect. We then discuss the problem of a DQD coupled to a high quality photonic resonator. When the photon correlation functions can be developed along a random-phase-approximation-like scheme, the response of the resonator gives an access to G({omega}).

  7. Quantum Device Applications of Mesoscopic Superconductivity

    NASA Astrophysics Data System (ADS)

    Hakonen, P. J.

    2006-08-01

    A brief account is given on the possibilities of mesoscopic superconductivity in low-noise amplifier and detector applications. In particular, three devices will be described: 1) Bloch oscillating transistor (BOT), 2) Inductively-read superconducting Cooper pair transistor (L-SET), and 3) Quantum capacitive phase detector (C-SET). The BOT is a low-noise current amplifier while the L-SET and C-SET act as ultra-sensitive charge and phase detectors, respectively. The basic operating principles and the main characteristics of these devices will be reviewed and discussed.

  8. Toxicity testing and instream biological monitoring in evaluating municipal effluents

    SciTech Connect

    Krier, K.; Pontasch, K.

    1995-12-31

    Twelve streams receiving municipal wastewater treatment plant effluents were evaluated in riffle areas above and below the outfall using the Environmental Protection Agency`s Rapid Bioassessment Protocols (RBPs) for benthic macroinvertebrates. Eight of the sites evaluated using RBP 1 exhibited stream health in the downstream riffles equaling or exceeding the upstream riffles. RBP 1 results suggested possible impacts at the remaining four sites, and these sites were more intensely evaluated using RBPs 2 and 3, acute effluent toxicity tests with Daphnia magna, and quantification of periphytic chlorophyll a and ash free dry weight (AFDW). Results from RBP 2 indicated three of the four sites evaluated have similar taxonomic richness above and below the outfall, while one site is heavily impacted by organic pollutants. Toxicity tests with 100% effluent resulted in no mortality with any of the four effluents tested. Relative to the respective upstream sites, chlorophyll a was significantly increased at one downstream site and significantly reduced at another. AFDW was similar above and below the outfalls in all streams. These results suggest that laboratory toxicity tests may not always be adequate predictors of instream biological effects.

  9. An exact law can test biological theories of mortality.

    PubMed

    Azbel, Mark Ya

    2002-07-01

    Wild animals rarely grow old, and die due to extrinsic hazards. So, natural selection favors genes with good early effects even when they lead to senescence and death at later ages. This implies the Medawar accumulation of late-acting deleterious effects and Williams-Kirkwood life-history trade-off: mortality of a generation strongly depends on its early age life history. Human and protected animal populations live in evolutionary unprecedented conditions, and survive to old age. Quantitative analysis of their mortality establishes that in such conditions a dominant fraction of mortality yields an exact law. In contrast to mortality, the law is biologically non-specific (i.e. independent of genotypes, phenotypes, life history, old age diseases, and all other relevant factors, describing the population and its environment from conception to the age of death). It is universal for species as remote as humans and flies and may lead to the formulation of a biologically non-specific thermodynamic mechanism of mortality. The law predicts that mortality may be significantly decreased and reversed to its value at a much younger age. The reversal is consistent with demographic data. For instance, Swedish females, born in 1916, at 48 years restored the mortality rate they had at 20; Japanese females, born in 1927, at 28 restored the life expectancy they had 8 years earlier. The law quantitatively tests mortality theories and establishes their limitations.

  10. Membrane characteristics for biological blast overpressure testing using blast simulators.

    PubMed

    Alphonse, Vanessa D; Siva Sai Sujith Sajja, Venkata; Kemper, Andrew R; Rizel, Dave V; Duma, Stefan M; VandeVord, Pamela J

    2014-01-01

    Blast simulators often use passive-rupture membranes to generate shock waves similar to free-field blasts. The purpose of this study was to compare rupture patterns and pressure traces of three distinct membrane materials for biological and biomechanical blast studies. An Advanced Blast Simulator (ABS) located at the Center for Injury Biomechanics at Virginia Tech was used to test membrane characteristics. Acetate, Mylar, and aluminum sheets with different thicknesses were used to obtain pressures between 70–210 kPa. Static pressure was measured inside the tube at the test section using piezoelectric pressure sensors. Peak overpressure, positive duration, and positive impulse were calculated for each test. Rupture patterns and characteristic pressure traces were unique to each membrane type and thickness. Shock wave speed ranged between 1.2-1.8 Mach for static overpressures of 70–210 kPa. Acetate membranes fragmented sending pieces down the tube, but produced ideal (Friedlander) pressure traces. Mylar membranes bulged without fragmenting, but produced less-than-ideal pressure traces. Aluminum membranes did not fragment and produced ideal pressure traces. However, the cost of manufacturing and characterizing aluminum membranes should be considered during membrane selection. This study illustrates the advantages and disadvantages of using Mylar, acetate, and aluminum for passive rupture membranes for blast simulators.

  11. The Mesoscopic Electrochemistry of Molecular Junctions

    PubMed Central

    Bueno, Paulo R.; Benites, Tiago A.; Davis, Jason J.

    2016-01-01

    Within the context of an electron dynamic (time-dependent) perspective and a voltage driving force acting to redistribute electrons between metallic and addressable molecular states, we define here the associated electron admittance and conductance. We specifically present a mesoscopic approach to resolving the electron transfer rate associated with the electrochemistry of a redox active film tethered to metallic leads and immersed in electrolyte. The methodology is centred on aligning the lifetime of the process of electron exchange with associated resistance and capacitance quantities. Notably, however, these are no longer those empirically known as charge transfer resistance and pseudo-capacitance, but are those derived instead from a consideration of the quantum states contained in molecular films and their accessibility through a scattering region existing between them and the metallic probe. The averaged lifetime (τr) associated with the redox site occupancy is specifically dependent on scattering associated with the quantum channels linking them to the underlying metallic continuum and associated with both a quantum resistance (Rq) and an electrochemical (redox) capacitance (Cr). These are related to electron transfer rate through k = 1/τr = (RqCr)−1. The proposed mesoscopic approach is consistent with Marcus’s (electron transfer rate) theory and experimental measurements obtained by capacitance spectroscopy. PMID:26757677

  12. Mesoscopic Simulation Methods for Polymer Dynamics

    NASA Astrophysics Data System (ADS)

    Larson, Ronald

    2015-03-01

    We assess the accuracy and efficiency of mesoscopic simulation methods, namely Brownian Dynamics (BD), Stochastic Rotation Dynamics (SRD) and Dissipative Particle Dynamics (DPD), for polymers in solution at equilibrium and in flows in microfluidic geometries. Both SRD and DPD use solvent ``particles'' to carry momentum, and so account automatically for hydrodynamic interactions both within isolated polymer coils, and with other polymer molecules and with nearby solid boundaries. We assess quantitatively the effects of artificial particle inertia and fluid compressibility and show that they can be made small with appropriate choice of simulation parameters. We then use these methods to study flow-induced migration of polymer chains produced by: 1) hydrodynamic interactions, 2) streamline curvature or stress-gradients, and 3) convection of wall depletion zones. We show that huge concentration gradients can be produced by these mechanisms in microfluidic geometries that can be exploited for separation of polymers by size in periodic contraction-expansion geometries. We also assess the range of conditions for which BD, SRD or DPD is preferable for mesoscopic simulations. Finally, we show how such methods can be used to simulate quantitatively the swimming of micro-organisms such as E. coli. In collaboration with Lei Jiang and Tongyang Zhao, University of Michigan, Ann Arbor, MI.

  13. Mesoscopic superconductor as a ballistic quantum switch.

    SciTech Connect

    Melnikov, A. S.; Vinokur, V. M.; Materials Science Division; Russian Academy of Sciences

    2002-01-03

    Several key experiments have revealed a rich variety of vortex structures in mesoscopic superconductors in which only a few quanta of magnetic flux are trapped: these structures are polygon-like vortex 'molecules' and multi-quanta giant vortices. Ginzburg-Landau calculations confirmed second-order phase transitions between the giant vortex states and stable molecule-like configurations. Here we study theoretically the electronic structure and the related phase-coherent transport properties of such mesoscopic superconductor systems. The quasiparticle excitations in the vortices form coherent quantum-mechanical states that offer the possibility of controlling the phase-coherent transport through the sample by changing the number of trapped flux quanta and their configuration. The sample conductance measured in the direction of the applied magnetic field is determined by the transparency of multi-vortex configurations, which form a set of quantum channels. The transmission coefficient for each channel is controlled by multiple Andreev reflections within the vortex cores and at the sample edge. These interference phenomena result in a stepwise behaviour of the conductance as a function of the applied magnetic field, and we propose to exploit this effect to realize a vortex-based quantum switch where the magnetic field plays the role of the gate voltage.

  14. Computer simulations of granular materials: the effects of mesoscopic forces

    NASA Astrophysics Data System (ADS)

    Kohring, G. A.

    1994-12-01

    The problem of the relatively small angles of repose reported by computer simulations of granular materials is discussed. It is shown that this problem can be partially understood as resulting from mesoscopic forces which are commonly neglected in the simulations. After including mesoscopic forces, characterized by the easily measurable surface energy, 2D computer simulations indicate that the angle of repose should increase as the size of the granular grains decreases, an effect not seen without mesoscopic forces. The exact magnitude of this effect depends upon the value of the surface energy and the coordination number of the granular pile.

  15. Mesoscopic full counting statistics and exclusion models

    NASA Astrophysics Data System (ADS)

    Roche, P.-E.; Derrida, B.; Douçot, B.

    2005-02-01

    We calculate the distribution of current fluctuations in two simple exclusion models. Although these models are classical, we recover even for small systems such as a simple or a double barrier, the same distibution of current as given by traditional formalisms for quantum mesoscopic conductors. Due to their simplicity, the full counting statistics in exclusion models can be reduced to the calculation of the largest eigenvalue of a matrix, the size of which is the number of internal configurations of the system. As examples, we derive the shot noise power and higher order statistics of current fluctuations (skewness, full counting statistics, ....) of various conductors, including multiple barriers, diffusive islands between tunnel barriers and diffusive media. A special attention is dedicated to the third cumulant, which experimental measurability has been demonstrated lately.

  16. Mesoscopic magnetism and superconductivity: recent perspectives.

    SciTech Connect

    Basaran, Ali C.; Villegas, Javier E.; Jiang, J. S.; Hoffmann, Axel; Schuller, Ivan K.

    2015-11-01

    Mesoscopic Superconductivity and Magnetism at intermediate (“Mesoscopic”) length scales between atomic and bulk, have a long history of interesting new science. The existence of multiple length scales allows for the development of new science when different length scales become comparable to relevant geometric sizes. Different new phenomena appear due to topological interactions, geometric confinement, proximity between dissimilar materials, dimensional crossover, and collective effects induced by the periodicity. In this brief review we are not able to cover comprehensively this vast field. Instead we select a few recent exciting highlights, which illustrate the type of novel science which can be accomplished in superconducting and magnetic structures. Superconductors and magnetic materials can serve as model systems and provide new ideas, which can be extended to other systems such as ferroelectrics and multiferroics. In this paper we also highlight general open questions and new directions in which the field may move.

  17. Vortex phase separation in mesoscopic superconductors

    PubMed Central

    Iaroshenko, O.; Rybalko, V.; Vinokur, V. M.; Berlyand, L.

    2013-01-01

    We demonstrate that in mesoscopic type II superconductors with the lateral size commensurate with London penetration depth, the ground state of vortices pinned by homogeneously distributed columnar defects can form a hierarchical nested domain structure. Each domain is characterized by an average number of vortices trapped at a single pinning site within a given domain. Our study marks a radical departure from the current understanding of the ground state in disordered macroscopic systems and provides an insight into the interplay between disorder, vortex-vortex interaction, and confinement within finite system size. The observed vortex phase segregation implies the existence of the soliton solution for the vortex density in the finite superconductors and establishes a new class of nonlinear systems that exhibit the soliton phenomenon.

  18. Multi-scaling and mesoscopic structures

    PubMed Central

    Salje, E. K. H.

    2010-01-01

    Multi-scaling and the systematic investigation of mesoscopic structures represent a field of fruitful cooperation in physics, chemistry, mineralogy and life sciences. The increasing miniaturization of devices as well as the emphasis of recent research on microstructures with length scales of a few nanometres lead to paradigm changes that may impact not only on our scientific understanding of fine-grained structures but also on the way we will develop device materials in the future. Here the role of interfaces becomes more important, and developments in areas such as ‘domain boundary engineering’ are evidence of this scientific evolution. In addition, nano-porous materials are particularly important in geology and in the development of artificial bones and ultra-light metals. Some of these developments are reviewed in this paper. PMID:20123752

  19. Giant vortex state in mesoscopic superconductors

    NASA Astrophysics Data System (ADS)

    Cobacy García, Luis; Giraldo, Jairo

    2005-08-01

    Using the self-consistent solution of the nonlinear Ginzburg-Landau equations, the superconducting state of a type II mesoscopic cylinder and of an infinite thin sheet with a circular hole (antidot), in the presence of an homogeneous magnetic field is studied. Close to the third critical field, the magnetic field penetrates the sample in the form of a vortex around the axis of the cylinder or of the antidot. This result has been found previously by other authors. The vortex, called a giant vortex, can carry several flux quanta. The giant vortex is persistent when the state is metastable and evolves to the so called paramagnetic Meissner effect (PME) within the cylinder. The behaviour of this effect as a function of the Ginzburg-Landau (GL) parameter is studied and the results are discussed. Gibbs free energy, order parameter and magnetic induccion as a function of the applied field and of the GL parameter are also studied.

  20. Mesoscopic and continuum modelling of angiogenesis

    PubMed Central

    Spill, F.; Guerrero, P.; Alarcon, T.; Maini, P. K.; Byrne, H. M.

    2016-01-01

    Angiogenesis is the formation of new blood vessels from pre-existing ones in response to chemical signals secreted by, for example, a wound or a tumour. In this paper, we propose a mesoscopic lattice-based model of angiogenesis, in which processes that include proliferation and cell movement are considered as stochastic events. By studying the dependence of the model on the lattice spacing and the number of cells involved, we are able to derive the deterministic continuum limit of our equations and compare it to similar existing models of angiogenesis. We further identify conditions under which the use of continuum models is justified, and others for which stochastic or discrete effects dominate. We also compare different stochastic models for the movement of endothelial tip cells which have the same macroscopic, deterministic behaviour, but lead to markedly different behaviour in terms of production of new vessel cells. PMID:24615007

  1. Mesoscopic neurodynamics: from neuron to brain.

    PubMed

    Freeman, W J

    2000-01-01

    Intelligent behavior is characterized by flexible and creative pursuit of endogenously defined goals. Intentionality is a key concept by which to link neuron and brain to goal-directed behavior through brain dynamics. An archetypal form of intentional behavior is an act of observation in space-time, by which information is sought for the guidance of future action to explore unpredictable and ever-changing environments. These acts are based in the brain dynamics that creates spatiotemporal patterns of neural activity, serving as images of goals, of command sequences by which to act to reach goals, and of expected changes in sensory input resulting from intended actions. Prediction of the sensory consequences of intended action and evaluation of performance is by reafference. An intentional act is completed upon modification of the system by itself through learning. These principles are well known among psychologists and philosophers. What is new is the development of nonlinear mesoscopic brain dynamics, by which the theory of chaos can be used to understand and simulate the constructions of meaningful patterns of neural activity that implement the process of observation. The design of neurobiological experiments, analysis of the resulting data, and synthesis of explanatory models require an understanding of the hierarchical nature of brain organization, here conceived as single neurons and neural networks at the microscopic level; clinically defined cortical and subcortical systems studied by brain imaging (for example, fMRI) at the macroscopic level, and self-organizing neural populations at an intermediate mesoscopic level, at which synaptic interactions create novel activity patterns through nonlinear state transitions. The constructive neurodynamics of sensory cortices, when they are engaged in pattern recognition, is revealed by learning-dependent spatial patterns of amplitude modulation and by newly discovered radially symmetric spatial gradients of the phase

  2. Systematic parameter inference in stochastic mesoscopic modeling

    NASA Astrophysics Data System (ADS)

    Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em

    2017-02-01

    We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

  3. Equilibrium and shot noise in mesoscopic systems

    SciTech Connect

    Martin, T.

    1994-10-01

    Within the last decade, there has been a resurgence of interest in the study of noise in Mesoscopic devices, both experimentally and theoretically. Noise in solid state devices can have different origins: there is 1/f noise, which is believed to arise from fluctuations in the resistance of the sample due to the motion of impurities. On top of this contribution is a frequency independent component associated with the stochastic nature of electron transport, which will be the focus of this paper. If the sample considered is small enough that dephasing and inelastic effects can be neglected, equilibrium (thermal) and excess noise can be completely described in terms of the elastic scattering properties of the sample. As mentioned above, noise arises as a consequence of random processes governing the transport of electrons. Here, there are two sources of randomness: first, electrons incident on the sample occupy a given energy state with a probability given by the Fermi-Dirac distribution function. Secondly, electrons can be transmitted across the sample or reflected in the same reservoir where they came from with a probability given by the quantum mechanical transmission/reflection coefficients. Equilibrium noise refers to the case where no bias voltage is applied between the leads connected to the sample, where thermal agitation alone allows the electrons close to the Fermi level to tunnel through the sample. In general, equilibrium noise is related to the conductance of the sample via the Johnson-Nyquist formula. In the presence of a bias, in the classical regime, one expects to recover the full shot noise < {Delta}{sup 2}I >= 2I{Delta}{mu} as was observed a long time ago in vacuum diodes. In the Mesoscopic regime, however, excess noise is reduced below the shot noise level. The author introduces a more intuitive picture, where the current passing through the device is a superposition of pulses, or electron wave packets, which can be transmitted or reflected.

  4. Mesoscopic modelling of conducting and semiconducting polymers

    NASA Astrophysics Data System (ADS)

    Stoneham, A. M.; Ramos, Marta M. D.

    2001-03-01

    We present generalized Monte Carlo calculations to assess the effects of texture and related key factors on the properties of polymer-based light emitting diodes. We describe one class of mesoscopic model giving specific realizations of the polymer network. The model, with simple physically based rules, shows the effects of polymer structural order on current flow, trapping and radiative and non-radiative charge recombination within the polymer layer. Interactions between charges are included explicitly, as are image interactions with the electrodes. It is important that these Coulomb interactions are not simplified to an averaged space charge, since the local interactions can lead to effective trapping of charge, even in the absence of defective chains or impurity trapping. There proves to be an important role for trapping, in which charges are localized for times long compared with transit times. The competition between current flow, trapping and radiative and non-radiative charge recombination means that some of the trends are not intuitively obvious. For example, if radiative recombination occurs only on short polymer chains, as is the case for certain polymer systems, the internal efficiency appears to saturate for a concentration of these shorter luminescent chains of about 20-30%. As the proportion of shorter chains increases, trapping increases, whereas current efficiency decreases. Our approach provides a natural link between atomistic models of individual polymer molecules and the macroscopic descriptions of device modelling. Such mesoscopic models provide a means to design better film structures, and hence to optimize the effectiveness of new organic materials in a range of applications.

  5. Mesoscopic packing of disk-like building blocks in calcium silicate hydrate

    PubMed Central

    Yu, Zechuan; Zhou, Ao; Lau, Denvid

    2016-01-01

    At 100-nanometer length scale, the mesoscopic structure of calcium silicate hydrate (C-S-H) plays a critical role in determining the macroscopic material properties, such as porosity. In order to explore the mesoscopic structure of C-S-H, we employ two effective techniques, nanoindentation test and molecular dynamics simulation. Grid nanoindentation tests find different porosity of C-S-H in cement paste specimens prepared at varied water-to-cement (w/c) ratios. The w/c-ratio-induced porosity difference can be ascribed to the aspect ratio (diameter-to-thickness ratio) of disk-like C-S-H building blocks. The molecular dynamics simulation, with a mesoscopic C-S-H model, reveals 3 typical packing patterns and relates the packing density to the aspect ratio. Illustrated with disk-like C-S-H building blocks, this study provides a description of C-S-H structures in complement to spherical-particle C-S-H models at the sub-micron scale. PMID:27845376

  6. Tests of Level A Suits - Protection Against Chemical and Biological Warfare Agents and Simulants: Executive Summary

    DTIC Science & Technology

    1998-06-01

    Tests of Level A Suits – Protection Against Chemical and Biological Warfare Agents and Simulants: Executive Summary Richard B. Belmonte...AND SUBTITLE Test Results of Level A Suits – Protection Against Chemical and Biological Warfare Agents and Simulants: Executive Summary 5. FUNDING...words) Twelve Level A protective suits were tested for GB and HD permeation swatch testing using modified procedures of TOP

  7. Mesoscopic structural organization in triphilic room temperature ionic liquids.

    PubMed

    Russina, Olga; Lo Celso, Fabrizio; Di Michiel, Marco; Passerini, Stefano; Appetecchi, Giovanni Battista; Castiglione, Franca; Mele, Andrea; Caminiti, Ruggero; Triolo, Alessandro

    2013-01-01

    Room temperature ionic liquids are one of the most exciting classes of materials in the last decade. The interest for these low melting, ionic compounds stems from both their technological impact and the stimulating plethora of structural and dynamic peculiarities in the mesoscopic space-time scales. It is nowadays well-established that they are characterised by an enhanced degree of mesoscopic order originating from their inherent amphiphilicity. In this contribution we highlight the existence of a further degree of mesoscopic complexity when dealing with RTILs bearing a medium length fluorous tail: such triphilic materials (they simultaneously contain polar, hydrophobic and fluorophilic moieties that mutually segregate from each other) turn out to be highly structurally compartmentalised at the mesoscopic level, thus paving the way to new smart applications for this new class of RTILs.

  8. The dawn of mesoscopic approach in drug development.

    PubMed

    Giuliani, Alessandro

    2011-01-01

    The feeling of the reaching of a crucial turning point is shared by the whole spectrum of sciences. The main features of this turning point are basically identical across different disciplines and can be interpreted as a re-location of the most relevant level of explanation (and consequently intervention for more applicative fields) from the microscopic to the so called mesoscopic level. Here, the character of the mesoscopic approach in drug development field will be briefly commented.

  9. Emerging measurement techniques for studies of mesoscopic superconductors.

    SciTech Connect

    Rydh, A.; Tagliati, S.; Nilsson, R. A.; Xie, R.; Pearson, J. E.; Welp, U.; Kwok, W. K.; Divan, R.

    2008-01-01

    Experimental research on mesoscopic systems puts high demands on the measurement infrastructure, including measurement system with associated sample preparation, experimental design, measurement electronics, and data collection. Successful experiments require both the ability to manufacture small samples and to successfully and accurately study their novel properties. Here, we discuss some aspects and recent advancements of general measurement techniques that should benefit several characterization methods such as thermodynamic, magnetic, and transport studies of mesoscopic superconductors.

  10. Dormancy and Recovery Testing for Biological Wastewater Processors

    NASA Technical Reports Server (NTRS)

    Hummerick, Mary F.; Coutts, Janelle L.; Lunn, Griffin M.; Spencer, LaShelle; Khodadad, Christina L.; Birmele, Michele N.; Frances, Someliz; Wheeler, Raymond

    2015-01-01

    Resource recovery and recycling waste streams to usable water via biological water processors is a plausible component of an integrated water purification system. Biological processing as a pretreatment can reduce the load of organic carbon and nitrogen compounds entering physiochemical systems downstream. Aerated hollow fiber membrane bioreactors, have been proposed and studied for a number of years as an approach for treating wastewater streams for space exploration.

  11. Optomechanical tests of hydrated biological tissues subjected to laser shaping

    SciTech Connect

    Omel'chenko, A I; Sobol', E N

    2008-03-31

    The mechanical properties of a matrix are studied upon changing the size and shape of biological tissues during dehydration caused by weak laser-induced heating. The cartilage deformation, dehydration dynamics, and hydraulic conductivity are measured upon laser heating. The hydrated state and the shape of samples of separated fascias and cartilaginous tissues were controlled by using computer-aided processing of tissue images in polarised light. (laser biology)

  12. Testing the Capacity of the National Biological Dose Response Plan (NBDRP) EX40801

    DTIC Science & Technology

    2009-11-01

    Testing the capacity of the National Biological Dose Response Plan (NBDRP) EX40801 Ruth Wilkins, James McNamee, Hillary...2. REPORT TYPE 3. DATES COVERED 4. TITLE AND SUBTITLE Testing the capacity of the National Biological Dose Response Plan (NBDRP) EX40801 5a...Report July 2009 Page 2 of 11 Testing the capacity of the NBDRP

  13. Vestigial Biological Structures: A Classroom-Applicable Test of Creationist Hypotheses

    ERIC Educational Resources Information Center

    Senter, Phil; Ambrocio, Zenis; Andrade, Julia B.; Foust, Katanya K.; Gaston, Jasmine E.; Lewis, Ryshonda P.; Liniewski, Rachel M.; Ragin, Bobby A.; Robinson, Khanna L.; Stanley, Shane G.

    2015-01-01

    Lists of vestigial biological structures in biology textbooks are so short that some young-Earth creationist authors claim that scientists have lost confidence in the existence of vestigial structures and can no longer identify any verifiable ones. We tested these hypotheses with a method that is easily adapted to biology classes. We used online…

  14. Vestigial Biological Structures: A Classroom-Applicable Test of Creationist Hypotheses

    ERIC Educational Resources Information Center

    Senter, Phil; Ambrocio, Zenis; Andrade, Julia B.; Foust, Katanya K.; Gaston, Jasmine E.; Lewis, Ryshonda P.; Liniewski, Rachel M.; Ragin, Bobby A.; Robinson, Khanna L.; Stanley, Shane G.

    2015-01-01

    Lists of vestigial biological structures in biology textbooks are so short that some young-Earth creationist authors claim that scientists have lost confidence in the existence of vestigial structures and can no longer identify any verifiable ones. We tested these hypotheses with a method that is easily adapted to biology classes. We used online…

  15. Metastable mesoscopic phases in concentrated protein solutions.

    PubMed

    Vekilov, Peter G

    2009-04-01

    The Gibbs's definition of a phase assumes completely homogeneous composition, with fluctuations bringing about local variations of less than a few percent. We apply light scattering, atomic force microscopy, and other techniques to demonstrate that even solutions of a single protein of moderate concentration do not comply with Gibbs's definition of phase. In such solutions clusters of sizes from several tens to several hundred nanometers exist and have limited lifetimes. These clusters have a higher free energy than the protein solution, and their lifetime is determined by the barrier for their decay. The clusters affect the viscous and viscoelastic behavior of the solution and are an essential part of potential condensation and aggregation pathways. Since the clusters are observed in solutions of single proteins, they indicate that the proteins have an intrinsic propensity to form mesoscopic structures, which is probably utilized in the formation of the protein complexes in the cytosol. Cluster theories developed for colloid systems appear inapplicable to proteins due to the high level of implied Coulomb repulsion. The experimental evidence on the clusters suggests that their sizes are determined by the kinetics of growth and decay, and not by thermodynamics. A microscopic theory to account for stabilizing and destabilizing factors involving protein molecules and solvent inside the clusters has not yet been developed.

  16. Dissipation in ferrofluids: mesoscopic versus hydrodynamic theory.

    PubMed

    Müller, H W; Engel, A

    1999-12-01

    Part of the field dependent dissipation in ferrofluids occurs due to the rotational motion of the ferromagnetic grains relative to the viscous flow of the carrier fluid. The classical theoretical description due to Shliomis (Zh. Eksp. Teor. Fiz. 61, 2411 (1971) [Sov. Phy JETP 34, 1291 (1972)]) uses a mesoscopic treatment of the particle motion to derive a relaxation equation for the nonequilibrium part of the magnetization. Complementary, the hydrodynamic approach of Liu [Phys. Rev. Lett. 70, 3580 (1993)] involves only macroscopic quantities and results in dissipative Maxwell equations for the magnetic fields in the ferrofluid. Different stress tensors and constitutive equations lead to deviating theoretical predictions in those situations, where the magnetic relaxation processes cannot be considered instantaneous on the hydrodynamic time scale. We quantify these differences for two situations of experimental relevance, namely, a resting fluid in an oscillating oblique field and the damping of parametrically excited surface waves. The possibilities of an experimental differentiation between the two theoretical approaches is discussed.

  17. The mesoscopic dynamics of thermodynamic systems.

    PubMed

    Reguera, D; Rubí, J M; Vilar, J M G

    2005-11-24

    Concepts of everyday use such as energy, heat, and temperature have acquired a precise meaning after the development of thermodynamics. Thermodynamics provides the basis for understanding how heat and work are related and the general rules that the macroscopic properties of systems at equilibrium follow. Outside equilibrium and away from macroscopic regimes, most of those rules cannot be applied directly. Here we present recent developments that extend the applicability of thermodynamic concepts deep into mesoscopic and irreversible regimes. We show how the probabilistic interpretation of thermodynamics together with probability conservation laws can be used to obtain Fokker-Planck equations for the relevant degrees of freedom. This approach provides a systematic method to obtain the stochastic dynamics of a system directly from its equilibrium properties. A wide variety of situations can be studied in this way, including many that were thought to be out of reach of thermodynamic theories, such as nonlinear transport in the presence of potential barriers, activated processes, slow relaxation phenomena, and basic processes in biomolecules, such as translocation and stretching.

  18. Interacting mesoscopic capacitor out of equilibrium

    NASA Astrophysics Data System (ADS)

    Litinski, Daniel; Brouwer, Piet W.; Filippone, Michele

    2017-08-01

    We consider the full nonequilibrium response of a mesoscopic capacitor in the large transparency limit, exactly solving a model with electron-electron interactions appropriate for a cavity in the quantum Hall regime. For a cavity coupled to the electron reservoir via an ideal point contact, we show that the response to any time-dependent gate voltage Vg(t ) is strictly linear in Vg. We analyze the charge and current response to a sudden gate voltage shift and find that this response is not captured by a simple circuit analogy. In particular, in the limit of strong interactions a sudden change in the gate voltage leads to the emission of a sequence of multiple charge pulses, the width and separation of which are controlled by the charge-relaxation time τc=h Cg/e2 and the time of flight τf. We also consider the effect of a finite reflection amplitude in the point contact, which leads to nonlinear-in-gate-voltage corrections to the charge and current response.

  19. Observation and Spectrum of Mesoscopic Buckling Modes

    NASA Astrophysics Data System (ADS)

    Carr, Stephen; Lawrence, Walter; Wybourne, Martin

    2004-03-01

    Classical Euler buckling of a rod or beam is a familiar phenomenon. For clamped-clamped boundary conditions the expected eigenfunction has a single antinode midway between the endpoints [1]. Recently we have observed stable higher-order buckling modes of suspended mesoscopic SiO2 beams [2], where the beam dimensions are approximately 200 nm x 500 nm in cross-section and 5 um to 60 um in length. Starting with a silicon wafer with 500 nm of thermal oxide, the suspended structures are fabricated by e-beam lithography and plasma etching. During the plasma etching of the underlying silicon, the structures buckle due to the residual strain from the thermal oxide growth. We have analyzed the observed elastic buckling spectrum in terms of clamped eigenfunctions with mode numbers n=1 through n=6 using image processing of the SEM micrographs. The observed spectrum exhibits several interesting features, including significant mode-mode interaction and the appearance of a geometrical constraint involving a sum over all modes. Ideal Euler buckling theory cannot account for the stability and interaction of the higher-order modes. We are investigating the applicability of a mulitmode Ginzburg-Landau description which includes ideal Euler buckling as a limiting case [3]. [1] S.M. Carr and M.N. Wybourne, Applied Physics Letters 82 709 (2003). [2] S.M. Carr, W.E. Lawrence, and M.N. Wybourne, submitted (2003). [3] W.E. Lawrence, APS March Meeting Bulletin (2004).

  20. Mesoscopic magnetomechanical hysteresis in a magnetorheological elastomer

    NASA Astrophysics Data System (ADS)

    Biller, A. M.; Stolbov, O. V.; Raikher, Yu. L.

    2015-08-01

    Field-induced magnetostatic interaction in a pair of identical particles made of a magnetically soft ferromagnet is studied. It is shown that due to saturation of the ferromagnet magnetization, this case differs significantly from the (super)paramagnetic one. A numerical solution is given, discussed, and compared with that provided by a simpler model (nonlinear mutual dipoles). We show that for multidomain ferromagnetic particles embedded in an elastomer matrix, as for paramagnetic ones in the same environment, pair clusters may form or break by a hysteresis scenario. However, the magnetization saturation brings in important features to this effect. First, the bistability state and the hysteresis take place only in a limited region of the material parameters of the system. Second, along with the hysteresis jumps occurring under the sole influence of the field, the "latent" hysteresis is possible which realizes only if the action of the field is combined with some additional (nonmagnetic) external factor. The obtained conditions, when used to assess the possibility of clustering in real magnetorheological polymers, infer an important role of mesoscopic magnetomechanical hysteresis for the macroscopic properties of these composites.

  1. Mesoscopic hydrothermodynamics of complex-structured materials

    NASA Astrophysics Data System (ADS)

    Vasconcellos, Áurea R.; Silva, A. A. P.; Luzzi, Roberto; Casas-Vázquez, J.; Jou, David

    2013-10-01

    Some experimental results in the study of disordered systems, polymeric fluids, solutions of micelles and surfactants, ionic-glass conductors, and others show a hydrodynamic behavior labeled “anomalous” with properties described by some kind of fractional power laws in place of the standard ones. This is a consequence of the fractal-like structure that is present in these systems of which we do not have a detailed description, thus impairing the application of the conventional ensemble formalism of statistical mechanics. In order to obtain a physical picture of the phenomenon for making predictions which may help with technological and industrial decisions, one may resort to different styles (so-called nonconventional) in statistical mechanics. In that way can be introduced a theory for handling such impaired situations, a nonconventional mesoscopic hydrothermodynamics (MHT). We illustrate the question presenting an application in a contracted description of such nonconventional MHT, consisting in the use of the Renyi approach to derive a set of coupled nonstandard evolution equations, one for the density, a nonconventional Maxwell-Cattaneo equation, which in a limiting case goes over a non-Fickian diffusion equation, and other for the velocity in fluids under forced flow. For illustration the theory is applied to the study of the hydrodynamic motion in several soft-matter systems under several conditions such as streaming flow appearing in electrophoretic techniques and flow generated by harmonic forces arising in optical traps. The equivalence with Lévy processes is discussed and comparison with experiment is done.

  2. Mesoscopic magnetomechanical hysteresis in a magnetorheological elastomer.

    PubMed

    Biller, A M; Stolbov, O V; Raikher, Yu L

    2015-08-01

    Field-induced magnetostatic interaction in a pair of identical particles made of a magnetically soft ferromagnet is studied. It is shown that due to saturation of the ferromagnet magnetization, this case differs significantly from the (super)paramagnetic one. A numerical solution is given, discussed, and compared with that provided by a simpler model (nonlinear mutual dipoles). We show that for multidomain ferromagnetic particles embedded in an elastomer matrix, as for paramagnetic ones in the same environment, pair clusters may form or break by a hysteresis scenario. However, the magnetization saturation brings in important features to this effect. First, the bistability state and the hysteresis take place only in a limited region of the material parameters of the system. Second, along with the hysteresis jumps occurring under the sole influence of the field, the "latent" hysteresis is possible which realizes only if the action of the field is combined with some additional (nonmagnetic) external factor. The obtained conditions, when used to assess the possibility of clustering in real magnetorheological polymers, infer an important role of mesoscopic magnetomechanical hysteresis for the macroscopic properties of these composites.

  3. Video and HTML: Testing Online Tutorial Formats with Biology Students

    ERIC Educational Resources Information Center

    Craig, Cindy L.; Friehs, Curt G.

    2013-01-01

    This study compared two common types of online information literacy tutorials: a streaming media tutorial using animation and narration and a text-based tutorial with static images. Nine sections of an undergraduate biology lab class (234 students total) were instructed by a librarian on how to use the BIOSIS Previews database. Three sections…

  4. Video and HTML: Testing Online Tutorial Formats with Biology Students

    ERIC Educational Resources Information Center

    Craig, Cindy L.; Friehs, Curt G.

    2013-01-01

    This study compared two common types of online information literacy tutorials: a streaming media tutorial using animation and narration and a text-based tutorial with static images. Nine sections of an undergraduate biology lab class (234 students total) were instructed by a librarian on how to use the BIOSIS Previews database. Three sections…

  5. Should soil testing services measure soil biological activity

    USDA-ARS?s Scientific Manuscript database

    Health of agricultural soils depends largely on conservation management to promote soil organic C accumulation. Total soil organic C changes slowly, but active fractions are more dynamic. A key indicator of healthy soil is potential biological activity, which could be measured rapidly with soil te...

  6. Mesoscopic non-equilibrium thermodynamic analysis of molecular motors.

    PubMed

    Kjelstrup, S; Rubi, J M; Pagonabarraga, I; Bedeaux, D

    2013-11-28

    We show that the kinetics of a molecular motor fueled by ATP and operating between a deactivated and an activated state can be derived from the principles of non-equilibrium thermodynamics applied to the mesoscopic domain. The activation by ATP, the possible slip of the motor, as well as the forward stepping carrying a load are viewed as slow diffusion along a reaction coordinate. Local equilibrium is assumed in the reaction coordinate spaces, making it possible to derive the non-equilibrium thermodynamic description. Using this scheme, we find expressions for the velocity of the motor, in terms of the driving force along the spacial coordinate, and for the chemical reaction that brings about activation, in terms of the chemical potentials of the reactants and products which maintain the cycle. The second law efficiency is defined, and the velocity corresponding to maximum power is obtained for myosin movement on actin. Experimental results fitting with the description are reviewed, giving a maximum efficiency of 0.45 at a myosin headgroup velocity of 5 × 10(-7) m s(-1). The formalism allows the introduction and test of meso-level models, which may be needed to explain experiments.

  7. AN EVALUATIVE STUDY OF TEACHER CONSTRUCTED TEST ITEMS FOR BSCS BIOLOGY. FINAL REPORT.

    ERIC Educational Resources Information Center

    HETTICK, VERGIL; TURNER, GEORGE C.

    THIS STUDY PROVIDES A PORTFOLIO OF SEVERAL THOUSAND FIELD-TESTED MULTIPLE CHOICE TEST ITEMS COORDINATED WITH THE CHAPTERS OF THE BIOLOGICAL SCIENCES CURRICULUM STUDY (BSCS) YELLOW VERSION TEXTBOOK. THE ITEMS WERE DEVELOPED BY A TEAM OF HIGH SCHOOL BIOLOGY TEACHERS AND WERE EVALUATED UNDER CLASSROOM CONDITIONS WITH GRADE 10 STUDENTS. A…

  8. Transport in mesoscopic charge density wave systems

    NASA Astrophysics Data System (ADS)

    Visscher, Mark Ivar

    This thesis presents several theoretical studies on the electrical transport of charge density waves in mesoscopic systems. On this length scale the fields of mesoscopic physics and superconductivity merge with the physics of CDW's. The research is focussed on the demonstration of new (quantum) physics in both the quasi- particle and the collective transport modes. Using a Blonder-Tinkham-Klapwijk scattering approach, it is shown that the tunneling conductance reflects the local density of states, rather than the bulk density of states as in superconductors. The conductance depends also on the phase of the CDW relative to the interface. Characteristic oscillations remain present after an ensemble averaging. We investigate two types of Aharonov-Bohm effects in CDW conductors. It is noted that a parity effect exist for the number of electrons in the ring, which shifts the modulation of the observables with half of a flux quantum. The second problem addresses the collective CDW motion through an ensemble of columnar defects threaded by a magnetic flux. We show that the pinning properties of a single defect are periodically affected by the normal flux quantum. However, in an ensemble of uncorrelated Aharonov-Bohm rings, the effective (averaged) threshold field reflects a half flux quantum periodicity, similar to the Al'tshuler-Aronov-Spivak oscillations. These results are in qualitative agreement with experiments. We investigate the Josephson current through a superconductor-CDW-Superconductor (S/C/S) junction. For this system we formulate the kinetic equations within the Keldysh formalism. In the sliding regime, the narrow band noise frequency locks to the Josephson frequency. As a result, oscillations appear in the current-voltage characteristic, accompanied by plateaus in the collective CDW conductance. Furthermore, we investigate the 'Poor man's Josephson effect' in a C/N/C junction, in relation to the Josephson current through an S/N/S junction. The sliding

  9. Mesoscopic spin Hall effect in semiconductor nanostructures

    NASA Astrophysics Data System (ADS)

    Zarbo, Liviu

    The spin Hall effect (SHE) is a name given to a collection of diverse phenomena which share two principal features: (i) longitudinal electric current flowing through a paramagnetic semiconductor or metallic sample leads to transverse spin current and spin accumulation of opposite sign at opposing lateral edges; (ii) SHE does not require externally applied magnetic field or magnetic ordering in the equilibrium state of the sample, instead it relies on the presence of spin-orbit (SO) couplings within the sample. This thesis elaborates on a new type of phenomenon within the SHE family, predicted in our recent studies [Phys. Rev. B 72, 075361 (2005); Phys. Rev. Lett. 95, 046601 (2005); Phys. Rev. B 72, 075335 (2005); Phys. Rev. B 73 , 075303 (2006); and Europhys. Lett. 77, 47004 (2007)], where pure spin current flows through the transverse electrodes attached to a clean finitesize two-dimensional electron gas (2DEG) due to unpolarized charge current injected through its longitudinal leads. If transverse leads are removed, the effect manifests as nonequilibrium spin Hall accumulation at the lateral edges of 2DEG wires. The SO coupling driving this SHE effect is of the Rashba type, which arises due to structural inversion asymmetry of semiconductor heterostructure hosting the 2DEG. We term the effect "mesoscopic" because the spin Hall currents and accumulations reach optimal value in samples of the size of the spin precession length---the distance over which the spin of an electron precesses by an angle pi. In strongly SO-coupled structures this scale is of the order of ˜100 nm, and, therefore, mesoscopic in the sense of being much larger than the characteristic microscopic scales (such as the Fermi wavelength, screening length, or the mean free path in disordered systems), but still much smaller than the macroscopic ones. Although the first theoretical proposal for SHE, driven by asymmetry in SO-dependent scattering of spin-up and spin-down electrons off impurities

  10. Mesoscopic Conductance Fluctuations in Disordered Graphene

    NASA Astrophysics Data System (ADS)

    Bohra, Girish

    This thesis is focused on an experimental study of the fluctuations in the conductance of disordered graphene flakes. Conductance fluctuations (CF) are generated by varying either magnetic field (±8 T) or Fermi energy (via back-gate voltage) in both bilayer and single-layer graphene devices. A detailed comparative study of the conductance fluctuations at ultra-low temperatures (≤ 0.1 K), as a function of magnetic field and Fermi energy, is performed to address the question of whether mesoscopic transport in graphene is governed by similar theoretical principles as in regular dirty metals and semiconductors. This study reveals a dramatic deviation from ergodicity for the CF in graphene, according to which fluctuations generated by varying magnetic field are found to be much smaller than those obtained when sweeping Fermi energy. The CF also show a strongly anisotropic response to the symmetry-breaking effects of a magnetic field, applied perpendicular or parallel to the plane of the graphene sheet. An extensive study of the temperature dependence of CF is also performed (0.03 - 100 K), and further confirms the non-ergodic character of the CF in disordered graphene by showing two separate temperature cut-offs for magneto-CF and density-induced CF. The non-ergodic character and robust nature of density-induced CF suggests the complex and challenging nature of quantum interference in graphene, as compared to that in non-Dirac materials, emphasizing the need for development of more sophisticated theoretical models and a better understanding of substrate-induced disorder.

  11. Testing systems for biologic markers of genotoxic exposure and effect

    SciTech Connect

    Mendelsohn, M.L.

    1986-11-19

    Societal interest in genotoxicity stems from two concerns: the fear of carcinogenesis secondary to somatic mutation; and the fear of birth defects and decreasing genetic fitness secondary to heritable mutation. There is a pressing need to identify agents that can cause these effects, to understand the underlying dose-response relationships, to identify exposed populations, and to estimate both the magnitude of exposure and the risk of adverse health effects in such populations. Biologic markers refer either to evidence in surrogate organisms, or to the expressions of exposure and effect in human populations. 21 refs.

  12. Biologically Relevant Exposure Science for 21st Century Toxicity Testing

    EPA Science Inventory

    High visibility efforts in toxicity testing and computational toxicology including the recent NRC report, Toxicity Testing in the 21st Century: a Vision and Strategy (NRC, 2007), raise important research questions and opportunities for the field of exposure science. The authors ...

  13. Biologically Relevant Exposure Science for 21st Century Toxicity Testing

    EPA Science Inventory

    High visibility efforts in toxicity testing and computational toxicology including the recent NRC report, Toxicity Testing in the 21st Century: a Vision and Strategy (NRC, 2007), raise important research questions and opportunities for the field of exposure science. The authors ...

  14. LASER BIOLOGY: Optomechanical tests of hydrated biological tissues subjected to laser shaping

    NASA Astrophysics Data System (ADS)

    Omel'chenko, A. I.; Sobol', E. N.

    2008-03-01

    The mechanical properties of a matrix are studied upon changing the size and shape of biological tissues during dehydration caused by weak laser-induced heating. The cartilage deformation, dehydration dynamics, and hydraulic conductivity are measured upon laser heating. The hydrated state and the shape of samples of separated fascias and cartilaginous tissues were controlled by using computer-aided processing of tissue images in polarised light.

  15. CHAIRMEN'S FOREWORD: The Seventh International Conference on New Phenomena in Mesoscopic Structures & The Fifth International Conference on Surfaces and Interfaces of Mesoscopic Devices

    NASA Astrophysics Data System (ADS)

    Aoyagi, Yoshinobu; Goodnick, Stephen M.

    2006-05-01

    , non-equilibrium transport, instabilities, nano-electro-mechanical systems, mesoscopic Josephson effects, phase coherence and breaking, and the Kondo effect •Systems of nanodevices: Quantum cellular automata, systolic SET processors, quantum neural nets, adaptive effects in circuits, and molecular circuits •Nanomaterials: nanotubes, nanowires, organic and molecular materials, self-assembled nano wires, and organic devices •Nanobioelectronics: electronic properties of biological structures on the nanoscale. This year's conference was organized by Prof Stephen Goodnick, Arizona State University, and Prof Yoshinobu Aoyagi, Tokyo Institute of Technology. The conference benefited from 14 invited speakers, whose topics spanned the above list, and a total of 97 registered attendees. The largest contingent was from Japan, followed closely by the US. In total, there were 49 from Japan, 31 fiom the US, and 17 from Europe. The organizers want to especially thank the sponsors for the meeting: The Office of Naval Research, the Army Research Office, and Arizona State University on the US side, and the Japan Society for the Promotion of Science, through their 151 Committee, on the Japanese side. PROGRAM COMMITTEE •Prof Gerhard Abstreiter, Technical University of Munich •Prof Tsuneya Ando, Tokyo Institute of Technology •Prof John Barker, University of Glasgow •Prof Jonathan Bird, the University at Buffalo •Prof Robert Blick, University of Wisconsin •Prof David Ferry, Chair, Arizona State University •Dr Yoshiro Hirayama, NTT Basic Research Laboratories •Dr Koji Ishibashi, RIKEN •Prof Carlo Jacoboni, University of Modena •Prof David Janes, Purdue University •Prof Friedl Kuchar, University of Leoben •Prof K. Matsumoto, Osaka University •Prof Wolfgang Porod, Notre Dame University •Prof Michiharu Tabe, Shizuoka University •Prof Joachim Wolter, Eindhoven Institute of Technology •Prof Lukas Worschech, University of Würzburg •Dr Naoki Yokoyama, Fujitsu

  16. Reaction times to weak test lights. [psychophysics biological model

    NASA Technical Reports Server (NTRS)

    Wandell, B. A.; Ahumada, P.; Welsh, D.

    1984-01-01

    Maloney and Wandell (1984) describe a model of the response of a single visual channel to weak test lights. The initial channel response is a linearly filtered version of the stimulus. The filter output is randomly sampled over time. Each time a sample occurs there is some probability increasing with the magnitude of the sampled response - that a discrete detection event is generated. Maloney and Wandell derive the statistics of the detection events. In this paper a test is conducted of the hypothesis that the reaction time responses to the presence of a weak test light are initiated at the first detection event. This makes it possible to extend the application of the model to lights that are slightly above threshold, but still within the linear operating range of the visual system. A parameter-free prediction of the model proposed by Maloney and Wandell for lights detected by this statistic is tested. The data are in agreement with the prediction.

  17. Tests of Level B Suits - Protection Against Chemical and Biological Warfare Agents and Simulants: Executive Summary

    DTIC Science & Technology

    1999-04-01

    Tests of Level B Suits – Protection Against Chemical and Biological Warfare Agents and Simulants: Executive Summary Robert S. Lindsay April...Final; Jan 98 – Jun 98 4. TITLE AND SUBTITLE Tests of Level B Suits – Protection Against Chemical and Biological Warfare Agents and Simulants...Occupational Safety and Health Level B∗ suit designs were tested to assess their capability to protect in a chemical warfare agent

  18. High-Resolution Mesoscopic Fluorescence Molecular Tomography Based on Compressive Sensing

    PubMed Central

    Yang, Fugang; Ozturk, Mehmet S.; Zhao, Lingling; Cong, Wenxiang; Wang, Ge

    2017-01-01

    Mesoscopic fluorescence molecular tomography (MFMT) is new imaging modality aiming at 3-D imaging of molecular probes in a few millimeter thick biological samples with high-spatial resolution. In this paper, we develop a compressive sensing-based reconstruction method with l1-norm regularization for MFMT with the goal of improving spatial resolution and stability of the optical inverse problem. Three-dimensional numerical simulations of anatomically accurate microvasculature and real data obtained from phantom experiments are employed to evaluate the merits of the proposed method. Experimental results show that the proposed method can achieve 80 μm spatial resolution for a biological sample of 3 mm thickness and more accurate quantifications of concentrations and locations for the fluorophore distribution than those of the conventional methods. PMID:25137718

  19. [Fish silage prepared from fish species of shrimp by-catch. II. Biological test in broilers].

    PubMed

    Rodríguez, T; Montilla, J J; Bello, R A

    1990-12-01

    The purpose of this study was the nutritional evaluation of proteins in fish silage. A biological test was conducted in chicks (broilers) to evaluate two levels of inclusion of fish silage (2.5% and 5%, respectively) in diets normally used for feeding them. Chicks were evaluated in weight gain, food consumption, and feeding conversion index. Finally, flavor and acceptability tests of meat from broilers fed the experimental diet were conducted. Results of the biological assay indicated that the best biological response was that of the animals fed the 5% fish silage diet. Sensory tests revealed that the meat of chicks fed the experimental diets had favorable acceptance by the consumers.

  20. Biological Gender Differences in Students' Errors on Mathematics Achievement Tests

    ERIC Educational Resources Information Center

    Stewart, Christie; Root, Melissa M.; Koriakin, Taylor; Choi, Dowon; Luria, Sarah R.; Bray, Melissa A.; Sassu, Kari; Maykel, Cheryl; O'Rourke, Patricia; Courville, Troy

    2017-01-01

    This study investigated developmental gender differences in mathematics achievement, using the child and adolescent portion (ages 6-19 years) of the Kaufman Test of Educational Achievement-Third Edition (KTEA-3). Participants were divided into two age categories: 6 to 11 and 12 to 19. Error categories within the Math Concepts & Applications…

  1. Biological Gender Differences in Students' Errors on Mathematics Achievement Tests

    ERIC Educational Resources Information Center

    Stewart, Christie; Root, Melissa M.; Koriakin, Taylor; Choi, Dowon; Luria, Sarah R.; Bray, Melissa A.; Sassu, Kari; Maykel, Cheryl; O'Rourke, Patricia; Courville, Troy

    2017-01-01

    This study investigated developmental gender differences in mathematics achievement, using the child and adolescent portion (ages 6-19 years) of the Kaufman Test of Educational Achievement-Third Edition (KTEA-3). Participants were divided into two age categories: 6 to 11 and 12 to 19. Error categories within the Math Concepts & Applications…

  2. A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

    ERIC Educational Resources Information Center

    van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

    2011-01-01

    Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge…

  3. Expertise for Teaching Biology Situated in the Context of Genetic Testing

    ERIC Educational Resources Information Center

    van der Zande, Paul; Akkerman, Sanne F.; Brekelmans, Mieke; Waarlo, Arend Jan; Vermunt, Jan D.

    2012-01-01

    Contemporary genomics research will impact the daily practice of biology teachers who want to teach up-to-date genetics in secondary education. This article reports on a research project aimed at enhancing biology teachers' expertise for teaching genetics situated in the context of genetic testing. The increasing body of scientific knowledge…

  4. Expertise for Teaching Biology Situated in the Context of Genetic Testing

    ERIC Educational Resources Information Center

    van der Zande, Paul; Akkerman, Sanne F.; Brekelmans, Mieke; Waarlo, Arend Jan; Vermunt, Jan D.

    2012-01-01

    Contemporary genomics research will impact the daily practice of biology teachers who want to teach up-to-date genetics in secondary education. This article reports on a research project aimed at enhancing biology teachers' expertise for teaching genetics situated in the context of genetic testing. The increasing body of scientific knowledge…

  5. A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

    ERIC Educational Resources Information Center

    van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

    2011-01-01

    Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge…

  6. 77 FR 30887 - Amendments to Sterility Test Requirements for Biological Products; Correction

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-24

    ...The Food and Drug Administration (FDA) is correcting a final rule that appeared in the Federal Register of May 3, 2012. (77 FR 26162). The final rule provides manufacturers of biological products greater flexibility, as appropriate, and encourages use of the most appropriate and state-of-the-art test methods for assuring the safety of biological products. The rule was published with an......

  7. Australian Biology Test Item Bank, Years 11 and 12. Volume II: Year 12.

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

    This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

  8. Australian Biology Test Item Bank, Years 11 and 12. Volume I: Year 11.

    ERIC Educational Resources Information Center

    Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

    This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

  9. Mesoscopic structures reveal the network between the layers of multiplex data sets

    NASA Astrophysics Data System (ADS)

    Iacovacci, Jacopo; Wu, Zhihao; Bianconi, Ginestra

    2015-10-01

    Multiplex networks describe a large variety of complex systems, whose elements (nodes) can be connected by different types of interactions forming different layers (networks) of the multiplex. Multiplex networks include social networks, transportation networks, or biological networks in the cell or in the brain. Extracting relevant information from these networks is of crucial importance for solving challenging inference problems and for characterizing the multiplex networks microscopic and mesoscopic structure. Here we propose an information theory method to extract the network between the layers of multiplex data sets, forming a "network of networks." We build an indicator function, based on the entropy of network ensembles, to characterize the mesoscopic similarities between the layers of a multiplex network, and we use clustering techniques to characterize the communities present in this network of networks. We apply the proposed method to study the Multiplex Collaboration Network formed by scientists collaborating on different subjects and publishing in the American Physical Society journals. The analysis of this data set reveals the interplay between the collaboration networks and the organization of knowledge in physics.

  10. Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

    SciTech Connect

    Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.

    2015-07-07

    We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

  11. Mesoscopic structures reveal the network between the layers of multiplex data sets.

    PubMed

    Iacovacci, Jacopo; Wu, Zhihao; Bianconi, Ginestra

    2015-10-01

    Multiplex networks describe a large variety of complex systems, whose elements (nodes) can be connected by different types of interactions forming different layers (networks) of the multiplex. Multiplex networks include social networks, transportation networks, or biological networks in the cell or in the brain. Extracting relevant information from these networks is of crucial importance for solving challenging inference problems and for characterizing the multiplex networks microscopic and mesoscopic structure. Here we propose an information theory method to extract the network between the layers of multiplex data sets, forming a "network of networks." We build an indicator function, based on the entropy of network ensembles, to characterize the mesoscopic similarities between the layers of a multiplex network, and we use clustering techniques to characterize the communities present in this network of networks. We apply the proposed method to study the Multiplex Collaboration Network formed by scientists collaborating on different subjects and publishing in the American Physical Society journals. The analysis of this data set reveals the interplay between the collaboration networks and the organization of knowledge in physics.

  12. Noisy dynamics of magnetic flux in mesoscopic cylinders

    NASA Astrophysics Data System (ADS)

    Dajka, J.; Luczka, J.; Mierzejewski, M.; Hänggi, P.

    2006-02-01

    We study magnetic fluxes and currents in mesoscopic systems of cylindrical symmetry like rings, toroids and cylinders. We analyze the time evolution of the magnetic flux and the characteristic time of a formation of the ordered state. We investigate how, starting from some symmetric initial state, the magnetic flux or the current approach their corresponding asymptotic state.

  13. Real-time feedback control of a mesoscopic superposition

    SciTech Connect

    Jacobs, Kurt; Finn, Justin; Vinjanampathy, Sai

    2011-04-15

    We show that continuous real-time feedback can be used to track, control, and protect a mesoscopic superposition of two spatially separated wave packets. The feedback protocol is enabled by an approximate state estimator and requires two continuous measurements, performed simultaneously. For nanomechanical and superconducting resonators, both measurements can be implemented by coupling the resonators to superconducting qubits.

  14. GENERAL: Fluctuation of Mesoscopic RLC Circuit at Finite Temperature

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-Yan; Wang, Ji-Suo; Fan, Hong-Yi

    2008-09-01

    We consider the fluctuation of mesoscopic RLC circuit at finite temperature since a resistance always produces Joule heat when the circuit is working. By virtue of the thermo Geld dynamics and the coherent thermo state representation we show that the quantum mechanical zero-point fluctuations of both charge and current increase with the rising temperature and the resistance value.

  15. Cosmo Cassette: A Microfluidic Microgravity Microbial System For Synthetic Biology Unit Tests and Satellite Missions

    NASA Technical Reports Server (NTRS)

    Berliner, Aaron J.

    2013-01-01

    Although methods in the design-build-test life cycle of the synthetic biology field have grown rapidly, the expansion has been non-uniform. The design and build stages in development have seen innovations in the form of biological CAD and more efficient means for building DNA, RNA, and other biological constructs. The testing phase of the cycle remains in need of innovation. Presented will be both a theoretical abstraction of biological measurement and a practical demonstration of a microfluidics-based platform for characterizing synthetic biological phenomena. Such a platform demonstrates a design of additive manufacturing (3D printing) for construction of a microbial fuel cell (MFC) to be used in experiments carried out in space. First, the biocompatibility of the polypropylene chassis will be demonstrated. The novel MFCs will be cheaper, and faster to make and iterate through designs. The novel design will contain a manifold switchingdistribution system and an integrated in-chip set of reagent reservoirs fabricated via 3D printing. The automated nature of the 3D printing yields itself to higher resolution switching valves and leads to smaller sized payloads, lower cost, reduced power and a standardized platform for synthetic biology unit tests on Earth and in space. It will be demonstrated that the application of unit testing in synthetic biology will lead to the automatic construction and validation of desired constructs. Unit testing methodologies offer benefits of preemptive problem identification, change of facility, simplicity of integration, ease of documentation, and separation of interface from implementation, and automated design.

  16. 40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... FILL MATERIAL Evaluation and Testing § 230.61 Chemical, biological, and physical evaluation and testing... materials. This section provides some guidance in determining which test and/or evaluation procedures are... effects. The principal concerns of discharge of dredged or fill material that contain contaminants are...

  17. Modeling the Drug Discovery Process: The Isolation and Biological Testing of Eugenol from Clove Oil

    NASA Astrophysics Data System (ADS)

    Miles, William H.; Smiley, Patricia M.

    2002-01-01

    This experiment describes the isolation and biological testing of eugenol and neutral compounds from commercially available clove oil. By coupling the chemical separation of the components of clove oil (an experiment described in many introductory organic laboratory textbooks) with a simple antibiotic test, the students "discover" the biologically active compound in clove oil. This experiment models one of the primary methods used in the discovery of new pharmaceutical agents.

  18. A PCR detection method for testing Mycoplasma contamination of veterinary vaccines and biological products.

    PubMed

    Ingebritson, A L; Gibbs, C P; Tong, C; Srinivas, G B

    2015-02-01

    A rapid test method was developed for detecting mycoplasma contamination in veterinary biological products. The method reduces testing time by 2 weeks and shows comparable sensitivity to the current agar-based detection model. The primary goals for the development of the test were to reduce the testing time, incorporate a method that was easily adaptable across the veterinary biologics industry and reduce the subjective interpretation of results. We found that biological enrichment is necessary to maintain sensitivity of the detection method when compared to the standard culture-based test and that periodic sampling of enrichment cultures is essential to detect a wide variety of mycoplasma species that may be present as contaminants. The PCR detection method is comparable to the agar-based model and can reduce the overall testing time by up to 14 days.

  19. Dormancy and Recovery Testing for Biological Wastewater Processors

    NASA Technical Reports Server (NTRS)

    Hummerick, Mary E.; Coutts, Janelle L.; Lunn, Griffin M.; Spencer, LaShelle; Khodadad, Christina L.; Frances, Someliz; Wheller, Raymond

    2015-01-01

    Bioreactors, such as aerated membrane type bioreactors have been proposed and studied for a number of years as an alternate approach for treating wastewater streams for space exploration. Several challenges remain before these types of bioreactors can be used in space settings, including transporting the bioreactors with their microbial communities to space, whether that be the International Space Station or beyond, or procedures for safing the systems and placing them into dormant state for later start-up. Little information is available on such operations as it is not common practice for terrestrial systems. This study explored several dormancy processes for established bioreactors to determine optimal storage and recovery conditions. Procedures focused on complete isolation of the microbial communities from an operational standpoint and observing the effects of: 1) storage temperature, and 2) storage with or without the reactor bulk fluid. The first consideration was tested from a microbial integrity and power consumption standpoint; both room temperature (25 C) and cold (4 C) storage conditions were studied. The second consideration was explored; again, for microbial integrity as well as plausible real-world scenarios of how terrestrially established bioreactors would be transported to microgravity and stored for periods of time between operations. Biofilms were stored without the reactor bulk fluid to simulate transport of established biofilms into microgravity, while biofilms stored with the reactor bulk fluid simulated the most simplistic storage condition to implement operations for extended periods of nonuse. Dormancy condition did not have an influence on recovery in initial studies with immature biofilms (48 days old), however, a lengthy recovery time was required (20+ days). Bioreactors with fully established biofilms (13 months) were able to recover from a 7-month dormancy period to steady state operation within 4 days (approximately 1 residence cycle

  20. Dormancy and Recovery Testing for Biological Wastewater Processors

    NASA Technical Reports Server (NTRS)

    Hummerick, Mary E.; Coutts, Janelle L.; Lunn, Griffin M.; Spencer, LaShelle; Khodadad, Christina L.; Birmele, Michele N.; Frances, Someliz; Wheeler, Raymond

    2015-01-01

    Bioreactors, such as the aerated hollow fiber membrane type, have been proposed and studied for a number of years as an alternate approach for treating wastewater streams for space exploration. Several challenges remain to be resolved before these types of bioreactors can be used in space settings, including transporting the bioreactors with intact and active biofilms, whether that be to the International Space Station or beyond, or procedures for safing the systems and placing them into a dormant state for later start-up. Little information is available on such operations as it is not common practice for terrestrial systems. This study explored several dormancy processes for established bioreactors to determine optimal storage and recovery conditions. Procedures focused on complete isolation of the microbial communities from an operational standpoint and observing the effects of: 1) storage temperature, and 2) storage with or without the reactor bulk fluid. The first consideration was tested from a microbial integrity and power consumption standpoint; both ambient temperature (25 C) and cold (4 C) storage conditions were studied. The second consideration was explored; again, for microbial integrity as well as plausible real-world scenarios of how terrestrially established bioreactors would be transported to microgravity and stored for periods of time between operations. Biofilms were stored without the reactor bulk fluid to simulate transport of established biofilms into microgravity, while biofilms stored with the reactor bulk fluid simulated the most simplistic storage condition to implement operations for extended periods of nonuse. Dormancy condition did not have an influence on recovery in initial studies with immature biofilms (48 days old), however a lengthy recovery time was required (20+ days). Bioreactors with fully established biofilms (13 months) were able to recover from a 7-month dormancy period to steady state operation within 4 days (approx. 1

  1. Recent advances in sensitized mesoscopic solar cells.

    PubMed

    Grätzel, Michael

    2009-11-17

    -intensive high vacuum and materials purification steps that are currently employed in the fabrication of all other thin-film solar cells. Organic materials are abundantly available, so that the technology can be scaled up to the terawatt scale without running into feedstock supply problems. This gives organic-based solar cells an advantage over the two major competing thin-film photovoltaic devices, i.e., CdTe and CuIn(As)Se, which use highly toxic materials of low natural abundance. However, a drawback of the current embodiment of OPV cells is that their efficiency is significantly lower than that for single and multicrystalline silicon as well as CdTe and CuIn(As)Se cells. Also, polymer-based OPV cells are very sensitive to water and oxygen and, hence, need to be carefully sealed to avoid rapid degradation. The research discussed within the framework of this Account aims at identifying and providing solutions to the efficiency problems that the OPV field is still facing. The discussion focuses on mesoscopic solar cells, in particular, dye-sensitized solar cells (DSCs), which have been developed in our laboratory and remain the focus of our investigations. The efficiency problem is being tackled using molecular science and nanotechnology. The sensitizer constitutes the heart of the DSC, using sunlight to pump electrons from a lower to a higher energy level, generating in this fashion an electric potential difference, which can exploited to produce electric work. Currently, there is a quest for sensitizers that achieve effective harnessing of the red and near-IR part of sunlight, converting these photons to electricity better than the currently used generation of dyes. Progress in this area has been significant over the past few years, resulting in a boost in the conversion efficiency of the DSC that will be reviewed.

  2. Using biological data to test climate change refugia

    NASA Astrophysics Data System (ADS)

    Morelli, T. L.; Maher, S. P.

    2015-12-01

    The concept of refugia has been discussed from theoretical and paleontological perspectives to address how populations persisted during periods of unfavorable climate. Recently, several studies have applied the idea to contemporary landscapes to identify locations that are buffered from climate change effects so as to favor greater persistence of valued resources relative to other areas. Refugia are now being discussed among natural resource agencies as a potential adaptation option in the face of anthropogenic climate change. Using downscaled climate data, we identified hypothetical refugial meadows in the Sierra Nevada and then tested them using survey and genetic data from Belding's ground squirrel (Urocitellus beldingi) populations. We predicted that refugial meadows would show higher genetic diversity, higher rates of occupancy and lower rates of extirpation over time. At each step of the research, we worked with managers to ensure the largest impact. Although no panacea, identifying climate change refugia could be an important strategy for prioritizing habitats for management intervention in order to conserve populations. This research was supported by the California LCC, the Northeast Climate Science Center, and NSF.

  3. Test Operations Procedure (TOP) 10-2-022A Chemical Vapor and Aerosol System-Level Testing of Chemical/Biological Protective Suits

    DTIC Science & Technology

    2013-12-16

    Level Testing of Chemical/ Biological Protective Suits 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHORS 5d...designing and conducting tests estimating penetration of chemical agent vapor and aerosol simulant through chemical/ biological (CB) protective suit... Biological ; CB; Defense Testing 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT SAR 18. NUMBER OF PAGES 188 19a

  4. Thermomagnetic phenomena in mesoscopic and paramagnetically limited superconductors

    NASA Astrophysics Data System (ADS)

    Hettinger, Mengling

    The superconducting fluctuation effect, due to droplets of preformed Cooper pairs above the critical temperature Tc, governs the temperature dependence of kinetic coefficients in superconductors at the onset of the phase transition. The transverse thermoelectric response - Nernst effect - is particularly sensitive to the fluctuations, and the large Nernst signal found in the various superconducting materials has raised much debate on its connection to the origin of unconventional superconductivity. In this thesis, we present a systematic study of the electrical and thermomagnetic transport phenomena in mesoscopic and paramagnetically (Pauli) limited superconductors. In the first chapter of this thesis we concentrate on the study of mesoscopic effects on transport in superconductors. We find that long-range phase coherence developing close to Tc triggers a great amplification of mesoscopic fluctuations due to strong pairing correlations. As a result, mesoscopic conductance fluctuations cease to be universal and exhibit pronounced dependence on temperature. Despite the lack of universality, in the sense of random matrix theory classification, we have discovered a different kind of universality in terms of temperature dependence of fluctuating characteristics. We find that mesoscopic fluctuations of conductivity, transversal thermoelectric coefficient and diamagnetic susceptibility consistently display the same scaling with temperature close to Tc. We connect our results to the existing experimental measurements of conductance fluctuations in superconducting films. Experimental verification of the temperature scaling and the overall magnitude of the mesoscopic fluctuations of Nernst coefficient will provide a powerful tool for a better understanding of thermomagnetic transport phenomena in correlated systems. In the second chapter of this thesis we examine the electrical and thermal transport anomalies in the ultra-thin superconducting films in an external in

  5. Routine biological tests in self-poisoning patients: results from an observational prospective multicenter study.

    PubMed

    Reydel, Thomas; Callahan, Jean-Christophe; Verley, Laurent; Teiten, Christelle; Andreotti, Christophe; Claessens, Yann Erick; Missud, David; L'Her, Erwan; Le Roux, Gael; Lerolle, Nicolas

    2016-08-01

    Routine biological tests are frequently ordered in self-poisoning patients, but their clinical relevance is poorly studied. This is a prospective multicentric observational study conducted in the emergency departments and intensive care units of 5 university and nonuniversity French hospitals. Adult self-poisoning patients without severely altered vital status on admission were prospectively included. Routine biological test (serum electrolytes and creatinine, liver enzymes, bilirubin, blood cell count, prothrombin time) ordering and results were analyzed. A total of 1027 patients were enrolled (age, 40.2 ± 14 years; women, 61.5%); no patient died during the hospital stay. Benzodiazepine was suspected in more than 70% of cases; 65% (range, 48%-80%) of patients had at least 1 routine biological test performed. At least 1 abnormal test was registered in 23% of these patients. Three factors were associated with abnormal test results: age older than 40 years, male sex, and poisoning with a drug known to alter routine tests (ie, acetaminophen, NSAIDs, metformine, lithium). Depending on these factors, abnormal results ranged from 14% to 48%. Unexpected severe life-threatening conditions were recorded in 6 patients. Only 3 patients were referred to the intensive care unit solely because of abnormal test results. Routine biological tests are commonly prescribed in nonsevere self-poisoning patients. Abnormal results are frequent but their relevance at bedside remains limited. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Testing with Feedback Yields Potent, but Piecewise, Learning of History and Biology Facts

    ERIC Educational Resources Information Center

    Pan, Steven C.; Gopal, Arpita; Rickard, Timothy C.

    2016-01-01

    Does correctly answering a test question about a multiterm fact enhance memory for the entire fact? We explored that issue in 4 experiments. Subjects first studied Advanced Placement History or Biology facts. Half of those facts were then restudied, whereas the remainder were tested using "5 W" (i.e., "who, what, when, where",…

  7. Using Open-Book Tests to Strengthen the Study Skills of Community-College Biology Students

    ERIC Educational Resources Information Center

    Phillips, Gregory

    2006-01-01

    The author observed that students enrolled in first-year college biology courses often had weak study skills. This longitudinal study examined the use of open-book tests to encourage reading and to assess the improvement of college students' study skills. There was a statistically significant improvement from the initial test to the final test…

  8. Using Open-Book Tests to Strengthen the Study Skills of Community-College Biology Students

    ERIC Educational Resources Information Center

    Phillips, Gregory

    2006-01-01

    The author observed that students enrolled in first-year college biology courses often had weak study skills. This longitudinal study examined the use of open-book tests to encourage reading and to assess the improvement of college students' study skills. There was a statistically significant improvement from the initial test to the final test…

  9. A Computer-Aided Self-Testing System for Biological Psychology.

    ERIC Educational Resources Information Center

    Leiblum, M. D.; And Others

    1994-01-01

    Describes the production of a computer-aided, self-testing system for university students enrolled in a first-year course in biological psychology. Project aspects described include selection, acquisition and description of software; question banks and test structures; modes of use (computer or printed version); evaluation; and future plans. (11…

  10. Testing with Feedback Yields Potent, but Piecewise, Learning of History and Biology Facts

    ERIC Educational Resources Information Center

    Pan, Steven C.; Gopal, Arpita; Rickard, Timothy C.

    2016-01-01

    Does correctly answering a test question about a multiterm fact enhance memory for the entire fact? We explored that issue in 4 experiments. Subjects first studied Advanced Placement History or Biology facts. Half of those facts were then restudied, whereas the remainder were tested using "5 W" (i.e., "who, what, when, where",…

  11. A Computer-Aided Self-Testing System for Biological Psychology.

    ERIC Educational Resources Information Center

    Leiblum, M. D.; And Others

    1994-01-01

    Describes the production of a computer-aided, self-testing system for university students enrolled in a first-year course in biological psychology. Project aspects described include selection, acquisition and description of software; question banks and test structures; modes of use (computer or printed version); evaluation; and future plans. (11…

  12. Effects of Scoring by Section and Independent Scorers' Patterns on Scorer Reliability in Biology Essay Tests

    ERIC Educational Resources Information Center

    Ebuoh, Casmir N.; Ezeudu, S. A.

    2015-01-01

    The study investigated the effects of scoring by section, use of independent scorers and conventional patterns on scorer reliability in Biology essay tests. It was revealed from literature review that conventional pattern of scoring all items at a time in essay tests had been criticized for not being reliable. The study was true experimental study…

  13. Robust mesoscopic superposition of strongly correlated ultracold atoms

    SciTech Connect

    Hallwood, David W.; Ernst, Thomas; Brand, Joachim

    2010-12-15

    We propose a scheme to create coherent superpositions of annular flow of strongly interacting bosonic atoms in a one-dimensional ring trap. The nonrotating ground state is coupled to a vortex state with mesoscopic angular momentum by means of a narrow potential barrier and an applied phase that originates from either rotation or a synthetic magnetic field. We show that superposition states in the Tonks-Girardeau regime are robust against single-particle loss due to the effects of strong correlations. The coupling between the mesoscopically distinct states scales much more favorably with particle number than in schemes relying on weak interactions, thus making particle numbers of hundreds or thousands feasible. Coherent oscillations induced by time variation of parameters may serve as a 'smoking gun' signature for detecting superposition states.

  14. Pressure-responsive mesoscopic structures in room temperature ionic liquids.

    PubMed

    Russina, Olga; Lo Celso, Fabrizio; Triolo, Alessandro

    2015-11-28

    Among the most spectacular peculiarities of room temperature ionic liquids, their mesoscopically segregated structural organization keeps on attracting attention, due to its major consequences for the bulk macroscopic properties. Herein we use molecular dynamics simulations to explore the nm-scale architecture in 1-octyl-3-methylimidazolium tetrafluoroborate, as a function of pressure. This study reveals an intriguing new feature: the mesoscopic segregation in ionic liquids is characterized by a high level of pressure-responsiveness, which progressively vanishes upon application of high enough pressure. These results are in agreement with recent X-ray scattering data and are interpreted in terms of the microscopic organization. This new feature might lead to new methods of developing designer solvents for enhanced solvation capabilities and selectivity.

  15. The mesoscopic membrane with proteins (MesM-P) model

    NASA Astrophysics Data System (ADS)

    Davtyan, Aram; Simunovic, Mijo; Voth, Gregory A.

    2017-07-01

    We present the Mesoscopic Membrane with Proteins (MesM-P) model, an extension of a previously developed elastic membrane model for mesoscale simulations of lipid membranes. MesM-P employs a discrete mesoscopic quasi-particle approach to model protein-facilitated shape and topology changes of the lipid membrane on length and time scales inaccessible to all-atom and quasimolecular coarse-grained molecular dynamics simulations. We investigate the ability of MesM-P to model the behavior of large lipid vesicles as a function of bound protein density. We find four distinct mechanisms for protein aggregation on the surface of the membrane, depending on membrane stiffness and protein spontaneous curvature. We also establish a connection between MesM-P and the results of higher resolution coarse-grained molecular dynamics simulations.

  16. Multichiral ground states in mesoscopic p -wave superconductors

    NASA Astrophysics Data System (ADS)

    Becerra, V. Fernández; Milošević, M. V.

    2016-11-01

    Using Ginzburg-Landau formalism, we investigate the effect of confinement on the ground state of mesoscopic chiral p -wave superconductors in the absence of magnetic field. We reveal stable multichiral states with domain walls separating the regions with different chiralities, as well as monochiral states with spontaneous currents flowing along the edges. We show that multichiral states can exhibit identifying signatures in the spatial profile of the magnetic field if those are not screened by edge currents in the case of strong confinement. Such magnetic detection of domain walls in topological superconductors can serve as long-sought evidence of broken time-reversal symmetry. Furthermore, when applying electric current to mesoscopic p -wave samples, we found a hysteretic behavior in the current-voltage characteristic that distinguishes states with and without domain walls, thereby providing another useful hallmark for indirect confirmation of chiral p -wave superconductivity.

  17. Controlling the inhomogeneity of solid catalysts at the mesoscopic scale

    NASA Astrophysics Data System (ADS)

    Huang, Hua; Wada, Takahiro; Ariga, Hiroko; Takakusagi, Satoru; Asakura, Kiyotaka; Iwasawa, Yasuhiro

    2017-09-01

    High-performance catalysts are often composed of two or more active phases, which are believed to interact with each other at the mesoscopic scale structure. Unlike conventional powder catalysts flat surfaces is advantageous in that its surface structure can be precisely designed. We prepared precisely designed Sb2O4/VSbO4/Si catalysts containing Sb2O4 ribbons with finely controlled width and separation by electron lithography. We demonstrated that the acrolein generation rate on the catalysts was related to the width and separation of the Sb2O4 ribbons. This work shows the possibility to regulate catalyses by inhomogeneity of the surface structure at the mesoscopic level.

  18. Negative partial density of states in mesoscopic systems

    NASA Astrophysics Data System (ADS)

    Satpathi, Urbashi; Singha Deo, P.

    2016-12-01

    Since the experimental observation of quantum mechanical scattering phase shift in mesoscopic systems, several aspects of it have not yet been understood. The experimental observations have also accentuated many theoretical problems related to Friedel sum rule and negativity of partial density of states. We address these problems using the concepts of Argand diagram and Burgers circuit. We can prove the possibility of negative partial density of states in mesoscopic systems. Such a conclusive and general evidence cannot be given in one, two or three dimensions. We can show a general connection between phase drops and exactness of semi classical Friedel sum rule. We also show Argand diagram for a scattering matrix element can be of few classes based on their topology and all observations can be classified accordingly.

  19. Mesoscopic Fluctuations for the Thinned Circular Unitary Ensemble

    NASA Astrophysics Data System (ADS)

    Berggren, Tomas; Duits, Maurice

    2017-09-01

    In this paper we study the asymptotic behavior of mesoscopic fluctuations for the thinned Circular Unitary Ensemble. The effect of thinning is that the eigenvalues start to decorrelate. The decorrelation is stronger on the larger scales than on the smaller scales. We investigate this behavior by studying mesoscopic linear statistics. There are two regimes depending on the scale parameter and the thinning parameter. In one regime we obtain a CLT of a classical type and in the other regime we retrieve the CLT for CUE. The two regimes are separated by a critical line. On the critical line the limiting fluctuations are no longer Gaussian, but described by infinitely divisible laws. We argue that this transition phenomenon is universal by showing that the same transition and their laws appear for fluctuations of the thinned sine process in a growing box. The proofs are based on a Riemann-Hilbert problem for integrable operators.

  20. Vortex shells in mesoscopic triangles of amorphous superconducting thin films

    NASA Astrophysics Data System (ADS)

    Kokubo, N.; Miyahara, H.; Okayasu, S.; Nojima, T.

    2016-11-01

    Direct observation of vortex states confined in mesoscopic regular triangle dots of amorphous Mo-Ge thin films was made with a scanning superconducting quantum interference device microscope. The observed magnetic images illustrate clearly how vortices are distributed over the triangle dots by forming not only commensurate triangular clusters, but also unique patterns imposed by incommensurability. We discuss the results in terms of vortex shells and construct the packing sequence of vortices in the multiple shell structure.

  1. Novel Techniques for Quantum State Manipulation in Mesoscopic Systems

    DTIC Science & Technology

    2005-10-05

    coupling with a very high frequency bandwidth (~1 THz). The results, so far, demonstrate orbital excitations on the right-side quantum dots as a...identified as the presence or absence of a collective excitation of a mesoscopic ensemble of nuclear spins surrounding a single quantum dot. All...Lukin, Eugene Demler, “Disordered Bose - Einstein Condensates in Quasi One-Dimensional Magnetic Microtraps,” cond- mat/0307402, Phys.Rev.Lett, 92, 076802

  2. Vortex 'puddles' and magic vortex numbers in mesoscopic superconducting disks

    SciTech Connect

    Connolly, M. R.; Milosevic, M. V.; Bending, S. J.; Clem, J. R.; Tamegai, T.

    2009-01-01

    The magnetic properties of a superconducting disk change dramatically when its dimensions become mesoscopic. Unlike large disks, where the screening currents induced by an applied magnetic field are strong enough to force vortices to accumulate in a 'puddle' at the centre, in a mesoscopic disk the interaction between one of these vortices and the edge currents can be comparable to the intervortex repulsion, resulting in a destruction of the ordered triangular vortex lattice structure at the centre. Vortices instead form clusters which adopt polygonal and shell-like structures which exhibit magic number states similar to those of charged particles in a confining potential, and electrons in artificial atoms. We have fabricated mesoscopic high temperature superconducting Bi{sub 2}Sr{sub 2}CaCu{sub 2}O{sub 8+δ} disks and investigated their magnetic properties using magneto-optical imaging (MOI) and high resolution scanning Hall probe microscopy (SHPM). The temperature dependence of the vortex penetration field measured using MOI is in excellent agreement with models of the thermal excitation of pancake vortices over edge barriers. The growth of the central vortex puddle has been directly imaged using SHPM and magic vortex numbers showing higher stability have been correlated with abrupt jumps in the measured local magnetisation curves.

  3. Mesoscopic analysis of motion and conformation of cross-bridges.

    PubMed

    Borejdo, J; Rich, R; Midde, K

    2012-12-01

    The orientation of a cross-bridge is widely used as a parameter in determining the state of muscle. The conventional measurements of orientation, such as that made by wide-field fluorescence microscopy, electron paramagnetic resonance (EPR) or X-ray diffraction or scattering, report the average orientation of 10(12)-10(9) myosin cross-bridges. Under conditions where all the cross-bridges are immobile and assume the same orientation, for example in normal skeletal muscle in rigor, it is possible to determine the average orientation from such global measurements. But in actively contracting muscle, where a parameter indicating orientation fluctuates in time, the measurements of the average value provide no information about cross-bridge kinetics. To avoid problems associated with averaging information from trillions of cross-bridges, it is necessary to decrease the number of observed cross-bridges to a mesoscopic value (i.e. the value affected by fluctuations around the average). In such mesoscopic regimes, the averaging of the signal is minimal and dynamic behavior can be examined in great detail. Examples of mesoscopic analysis on skeletal and cardiac muscle are provided.

  4. Mesoscopic cell structure of relaxor ferroelectrics at morphotropic phase boundary

    NASA Astrophysics Data System (ADS)

    Ahn, Sang-Jin; Kim, Jong-Jean

    2003-03-01

    Mesoscopic cell structure of relaxor ferroelectrics at morphotropic phase boundary Sang-Jin Ahn and Jong-Jean Kim Physics Department, KAIST, Taejon 305-701, Korea Relaxor-based ferroelectrics such as PZN-xPT and PMN-xPT have drawn a great attention due to an observation of a huge piezoelectric coefficient and an ultra high strain level. Although the first principle calculations on the basis of a single perovskite unit cell structure could explain much of the experimental observations, recent observations of a complex mesoscopic ordering and a heterogeneous domain structure suggest a composite cell of many perovskite units as a basic building block. Raman scattering spectra and observed stoichiometry of PZN-xPT and PMN-xPT allow for only a random pile-up structure of the composite block cells. Our composite block cell needs 27 perovskite unit cells to satisfy the morphotropic phase boundary conditions of structural and compositional variations. Using this mesoscopic block cell model we calculate for allowed mixing concentrations x at morphotropic phase boundaries of relaxor ferroelectrics, which agree with observed values.

  5. Combining molecular dynamics with mesoscopic Green's function reaction dynamics simulations

    NASA Astrophysics Data System (ADS)

    Vijaykumar, Adithya; Bolhuis, Peter G.; ten Wolde, Pieter Rein

    2015-12-01

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  6. A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

    NASA Astrophysics Data System (ADS)

    van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

    2011-10-01

    Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge concerning genetic testing and the related consequences for decision-making indicate the societal relevance of such a situated learning approach. What content knowledge do biology teachers need for teaching genetics in the personal health context of genetic testing? This study describes the required content knowledge by exploring the educational practice and clinical genetic practices. Nine experienced teachers and 12 respondents representing the clinical genetic practices (clients, medical professionals, and medical ethicists) were interviewed about the biological concepts and ethical, legal, and social aspects (ELSA) of testing they considered relevant to empowering students as future health care clients. The ELSA suggested by the respondents were complemented by suggestions found in the literature on genetic counselling. The findings revealed that the required teacher knowledge consists of multiple layers that are embedded in specific genetic test situations: on the one hand, the knowledge of concepts represented by the curricular framework and some additional concepts (e.g. multifactorial and polygenic disorder) and, on the other hand, more knowledge of ELSA and generic characteristics of genetic test practice (uncertainty, complexity, probability, and morality). Suggestions regarding how to translate these characteristics, concepts, and ELSA into context-based genetics education are discussed.

  7. Establishing construct validity of the Biology I Subject Area Testing program in Mississippi

    NASA Astrophysics Data System (ADS)

    Philippoff, Christy Michelle Hollis

    Science education has undergone many revisions since it was permanently embedded in the country's educational curriculum at the end of the 19th century. Some of these revisions occurred as a direct result of the No Child Left Behind Act (NCLB). This legislation placed more accountability on schools than ever before by requiring that all students pass a series of standardized tests (USDE, 2010). High schools in Mississippi require four areas of standardized testing: English II, Algebra I, U.S. History, and Biology I (Wroten, 2008). The focus of this study is the Biology I Subject Area Test. In an effort to determine the validity of that test, this study explores the importance of the Mississippi Biology I content standards according to the importance ratings and frequency of use ratings by science professionals in Mississippi. The science professionals surveyed for this study were high school science teachers, college science professors and scientists in their professional settings. The science professionals' importance ratings were compared to the importance ratings placed on the content strands by the Mississippi Biology I Subject Area Test. To further determine the test's validity, it is also compared to the National Science Education Standards.

  8. An investigation on impacts of scheduling configurations on Mississippi biology subject area testing

    NASA Astrophysics Data System (ADS)

    Marchette, Frances Lenora

    The purpose of this mixed modal study was to compare the results of Biology Subject Area mean scores of students on a 4 x 4 block schedule, A/B block schedule, and traditional year-long schedule for 1A to 5A size schools. This study also reviewed the data to determine if minority or gender issues might influence the test results. Interviews with administrators and teachers were conducted about the type of schedule configuration they use and the influence that the schedule has on student academic performance on the Biology Subject Area Test. Additionally, this research further explored whether schedule configurations allow sufficient time for students to construct knowledge. This study is important to schools, teachers, and administrators because it can assist them in considering the impacts that different types of class schedules have on student performance and if ethnic or gender issues are influencing testing results. This study used the causal-comparative method for the quantitative portion of the study and constant comparative method for the qualitative portion to explore the relationship of school schedules on student academic achievement on the Mississippi Biology Subject Area Test. The aggregate means of selected student scores indicate that the Mississippi Biology Subject Area Test as a measure of student performance reveals no significant difference on student achievement for the three school schedule configurations. The data were adjusted for initial differences of gender, minority, and school size on the three schedule configurations. The results suggest that schools may employ various schedule configurations and expect student performance on the Mississippi Biology Subject Area Test to be unaffected. However, many areas of concern were identified in the interviews that might impact on school learning environments. These concerns relate to effective classroom management, the active involvement of students in learning, the adequacy of teacher education

  9. Bioinformatics for the synthetic biology of natural products: integrating across the Design–Build–Test cycle

    PubMed Central

    Currin, Andrew; Jervis, Adrian J.; Rattray, Nicholas J. W.; Swainston, Neil; Yan, Cunyu; Breitling, Rainer

    2016-01-01

    Covering: 2000 to 2016 Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted. PMID:27185383

  10. - and Mesoscopic Soft Condensed Matter Architectures on Semiconductor Surfaces

    NASA Astrophysics Data System (ADS)

    Samuilov, Vladimir; Seo, Young-Soo; Ksenevich, Vitaly; Galibert, Jean; Sokolov, John; Rafailovich, Miriam

    2003-03-01

    A novel and simple approach of self-organized fabrication of two dimensional mesoscopic networks with the feature size down to 50 nm has been developed. The technique is based on the self-organized patterning in a thin layer of complex liquid (polymer solution) in the presence of humid atmosphere. Two dimensional mesoscopic honeycomb-shaped carbon structures were produced by high temperature annealing of nitrocellulose precursors [1]. The polymer network was also utilized as a mask for further reactive ion etching of surfaces with epi-layer of GaAs [2,3] and GaAs/AlGaAs ? -doped heterostructures [4]. The electrical transport in the obtained structures was studied in a temperature range from 1.9 to 300 K and in pulsed magnetic fields up to 35 T. A crossover from the Mott variable range hopping to the Colomb-gap Efros-Shklovskii variable range hopping has been observed experimentally in mesoscopic carbon structures [1]. At low fields, ln(R/R0) is proportional to B2. In the intermediate range, the magnetoresistance is linear on B. At high temperatures, if the hopping distance is comparable to the localization length, the observed small negative magnetoresistance in our samples is consistent to the weak-localization picture. Magnetoresistance of patterned GaAs/AlGaAs ?-doped structures is negative [4], which is relater to quantum interference in hopping regime. At B=0, the resistance showed typical behavior of a two-dimensional hopping. Below about 20 K, the data followed the Mott variable-range-hopping mechanism for two dimensions. Also, we have used diblock-copolymer system, self-assembled with L-B technique, to produce nano-patterns. These structures were utilized as templates for introducing metal nanopatterns on semiconductor surfaces by reactive ion beam etching for magnetic storage systems [5] and DNA separation on a flat surface [6] devices. 1. V.A. Samuilov, J. Galibert, V.K. Ksenevich, V.J. Goldman, M. Rafailovich, J. Sokolov, I.A. Bashmakov, V.A. Dorosinets

  11. Gender Differences in Caribbean Students' Performance on a Test of Errors in Biological Labelling.

    ERIC Educational Resources Information Center

    Soyibo, Kola

    1999-01-01

    Discusses the performance of 11th-grade students from Barbados, Belize, Jamaica, St. Lucia, St. Vincent, and Trinidad (n=1216) on an Errors in Biological Labeling Test (EBLT). Concludes that performance was low in six categories of errors, and that girls performed significantly better on each category of error than did boys. Contains 15…

  12. Sound and Faulty Arguments Generated by Preservice Biology Teachers When Testing Hypotheses Involving Unobservable Entities.

    ERIC Educational Resources Information Center

    Lawson, Anton E.

    2002-01-01

    Investigates the responses of a sample of preservice biology teachers enrolled in a teaching methods course to a casual question about why water rose in a jar inverted over a burning candle placed in a pan of water by formulating and testing six hypotheses. (Contains 43 references.) (Author/YDS)

  13. Causal attributions of obese men and women in genetic testing: implications of genetic/biological attributions.

    PubMed

    Hilbert, Anja; Dierk, Jan-Michael; Conradt, Matthias; Schlumberger, Pia; Hinney, Anke; Hebebrand, Johannes; Rief, Winfried

    2009-09-01

    The present study sought to investigate genetic/biological attributions of obesity, their associations with a predisposition to obesity and their crossectional and longitudinal implications for weight regulation in obese individuals presenting for genetic testing and counselling. A total of 421 obese men and women underwent psychological and anthropometric assessment and a mutation screen of the melanocortin-4 receptor gene. At study entry, women revealed more genetic/biological attributions than men on the Revised Illness Perception Questionnaire adapted to obesity (86.2% versus 59.7%). Genetic/biological attributions of obesity were associated in both sexes with a family history of obesity, assessed through Stunkard's Figure Rating Scale. In both sexes, genetic/biological attributions were unrelated to weight regulation beliefs and behaviour (i.e. self-efficacy, controllability beliefs, restrained eating and physical activity), assessed through standardised questionnaires or interview at baseline and at six-month follow-up. In addition, causal attributions and weight regulation beliefs and behaviour were not predictive of body mass index at six-month follow-up. Overall, the results indicate that causal attributions of obesity to genetic/biological factors in obese individuals presenting for genetic screening and counselling are crossectionally and longitudinally unrelated to weight regulation and longer-term weight outcome. Those who attribute their obesity to genetic/biological factors likely have a familial obesity risk.

  14. [Contribution of biological tests in the evaluation of professional asthma (author's transl)].

    PubMed

    Biot, N; Grosclaude, M; Meyer, J L; Perrin-Fayolle, M

    1980-01-01

    The eventual difficulties of diagnosing professional asthma sometimes need the help of methods of complementary diagnosis. The histamine-release test and that of basophils granules liberation are studied in this work, concerning 12 substances with a suspected allergenic action (saw-dust, textile fibres, chemicals, products of plant origin). The histamine-release and granules liberation tests were performed according to the techniques described respectively by Lichtenstein and Benveniste. Both examinations were positive in a concording manner in 8 cases out of 12, but this positivity was difficult to interprete for etiopathogenic reasons. The study of the curve of histamine-release in relation with the dose of allergen used in the test nevertheless enables to differentiate two types of answers, one related to an allergic mechanism, the other to an irritative one. These observations led to the deduction that a positive granules liberation test could be due to a non allergic mechanism. Negativity in both tests does not allow the rejection of the part played by these substances into the genesis of respiratory signs. Indeed these tests only investigate one part of the mechanisms which can be involved: direct stimulation of vagal irritant receptors and the plain pharmacological reactions escape from this type of biological investigations. The biological tests studied in this work can be used in a complementary fashion in the etiological survey of professional asthma but they cannot replace the realistic tests, more reliable because they react whatever the etiopathogenic mechanism involved.

  15. Offer of rapid testing and alternative biological samples as practical tools to implement HIV screening programs.

    PubMed

    Parisi, Maria Rita; Soldini, Laura; Di Perri, Giovanni; Tiberi, Simon; Lazzarin, Adriano; Lillo, Flavia B

    2009-10-01

    Implementation of HIV testing has the objective to increase screening, identify and counsel persons with infection, link them to clinical services and reduce transmission. Rapid tests and/or alternative biological samples (like oral fluid) give the option for a better general consent in approaching screening, immediate referral of HIV positives to medical treatment and partner notification. We tested the performance characteristics of an oral fluid-based rapid HIV test (Rapidtest HIV lateral flow-Healthchem diag. LLC) in comparison with routinely utilized methods in a selected population of known positive (N = 121) or negative (N = 754) subjects. The sensitivity of the rapid test was 99.1% (one false negative sample) and the specificity 98.8%. Five negatives showed a faint reactivity, 3 of these were reactive also in the reference test, one with a p24 only reaction in Western blot. If these 3 samples were excluded from the analysis the specificity increases to 99.2%. Results from our study confirm that, although a continuous improvement of the test performance is still needed to minimize false negative and positive results, rapid test and alternative biological samples may contribute to HIV prevention strategies by reaching a larger population particularly when and where regular screening procedures are difficult to obtain.

  16. Legal, workplace, and treatment drug testing with alternate biological matrices on a global scale.

    PubMed

    Cone, E J

    2001-09-15

    Global trends in drug trafficking and drug usage patterns indicate a continuing pattern of escalation throughout the world. Over the last two decades, urinalysis has evolved into a highly accurate means for determining whether individuals have been exposed to illicit drugs of abuse. Advances have also been made in the use of alternate biological matrices such as hair, oral fluids and sweat for drug testing. Often, these new matrices demonstrate some distinct advantages over urinalysis, e.g. less invasive procedures, different time course of drug detection. They may even indicate impairment. National and local laws of each country provide the underpinnings of drug-testing programs, but most countries have not addressed use of these alternate matrices. Currently, only a few countries have statutes that specifically mention use of alternate biological matrices, e.g. United States (Florida state law), Germany, Ireland, Poland and the Czech Republic. Conversely, few countries have prohibited collection of alternate biological specimens or drug test devices that utilize such specimens. In addition, guidelines for implementing drug testing programs have been slow to emerge and most deal primarily with workplace drug testing programs, e.g. United States. Currently, scientific technology utilized in drug testing is advancing rapidly, but there is a clear need for parallel development of guidelines governing the use of alternate matrices for drug testing. This article provides an overview of global drug trafficking patterns and drug use, and results from a survey of legal statutes in 20 countries covering use of alternate matrices for drug testing. In addition, elements needed for the development of guidelines for alternate matrices testing for drugs of abuse are discussed, and specific examples of use of alternate matrices in treatment monitoring are provided.

  17. Sprayed P25 scaffolds for high-efficiency mesoscopic perovskite solar cells.

    PubMed

    Huang, Haibo; Shi, Jiangjian; Lv, Songtao; Li, Dongmei; Luo, Yanhong; Meng, Qingbo

    2015-06-28

    Uniform, thickness-controllable and large-size mesoscopic TiO2 films based on commercial P25 nanoparticles are prepared by a spray method, which have been applied in the perovskite solar cells, achieving a high efficiency of 16%. This spray method shows promising application in the large-scale production of mesoscopic solar cells.

  18. Biology, host specificity tests, and risk assessment of the sawfly Heteroperreyia hubrichi, a potential biological control agent of Schinus terebinthifolius in Hawaii

    USDA-ARS?s Scientific Manuscript database

    Abstract. Heteroperreyia hubrichi Malaise (Hymenoptera: Pergidae), a foliage feeding sawfly of Schinus terebinthifolius Raddi (Sapindales: Anacardiaceae), was studied to assess its suitability as a classical biological control agent of this invasive weed in Hawaii. Nochoice host-specificity tests we...

  19. Proximity effect thermometer for local temperature measurements on mesoscopic samples.

    SciTech Connect

    Aumentado, J.; Eom, J.; Chandrasekhar, V.; Baldo, P. M.; Rehn, L. E.; Materials Science Division; Northwestern Univ; Univ. of Chicago

    1999-11-29

    Using the strong temperature-dependent resistance of a normal metal wire in proximity to a superconductor, we have been able to measure the local temperature of electrons heated by flowing a direct-current (dc) in a metallic wire to within a few tens of millikelvin at low temperatures. By placing two such thermometers at different parts of a sample, we have been able to measure the temperature difference induced by a dc flowing in the samples. This technique may provide a flexible means of making quantitative thermal and thermoelectric measurements on mesoscopic metallic samples.

  20. Fabrication and measurement of multi-terminal mesoscopic Josephson junctions

    NASA Astrophysics Data System (ADS)

    Solovyeva, Natalya; Tetsuya, Mishima; Santos, Michael; Shabani, Javad; Manucharyan, Vladimir

    We present fabrication and characterization of 3- and 4-terminal mesoscopic Josephson junctions involving InAs quantum well heterostructures and superconducting Al contacts. A cross-shaped nanowire junction region with dimensions of order a few 100 nm is dry-etched in the 2DEG, followed by deposition of superconducting contacts and gating electrodes. These novel 0D devices have been recently predicted to have topological features in their Andreev spectra and finite-bias transport; they may also be useful in efforts towards observation and braiding of Majorana fermions in the solid state. // This material is based upon work supported by the NSF under Grant No. DMR-1207537.

  1. Gravitational waves from mesoscopic dynamics of the extra dimensions

    PubMed

    Hogan

    2000-09-04

    Recent models which describe our world as a brane embedded in a higher dimensional space introduce new geometrical degrees of freedom, associated with spatial variations in the position of the brane and the size of the extra dimensions, that can be coherently excited by symmetry breaking in the early universe even on "mesoscopic" scales as large as 1 mm. The characteristic frequency and intensity of resulting gravitational radiation backgrounds are estimated. Extra dimensions with scale between 10(-14) and 1 mm can produce detectable backgrounds at frequencies f approximately 10(3) to 10(-4) Hz.

  2. A mesoscopic network model for permanent set in crosslinked elastomers

    SciTech Connect

    Weisgraber, T H; Gee, R H; Maiti, A; Clague, D S; Chinn, S; Maxwell, R S

    2009-01-29

    A mesoscopic computational model for polymer networks and composites is developed as a coarse-grained representation of the composite microstructure. Unlike more complex molecular dynamics simulations, the model only considers the effects of crosslinks on mechanical behavior. The elastic modulus, which depends only on the crosslink density and parameters in the bond potential, is consistent with rubber elasticity theory, and the network response satisfies the independent network hypothesis of Tobolsky. The model, when applied to a commercial filled silicone elastomer, quantitatively reproduces the experimental permanent set and stress-strain response due to changes in the crosslinked network from irradiation.

  3. Unraveling the Mesoscopic Character of Quantum Dots in Nanophotonics.

    PubMed

    Tighineanu, P; Sørensen, A S; Stobbe, S; Lodahl, P

    2015-06-19

    We provide a microscopic theory for semiconductor quantum dots that explains the pronounced deviations from the prevalent point-dipole description that were recently observed in spectroscopic experiments on quantum dots in photonic nanostructures. The deviations originate from structural inhomogeneities generating a large circular quantum current density that flows inside the quantum dot over mesoscopic length scales. The model is supported by the experimental data, where a strong variation of the multipolar moments across the emission spectrum of quantum dots is observed. Our work enriches the physical understanding of quantum dots and is of significance for the fields of nanophotonics, quantum photonics, and quantum-information science, where quantum dots are actively employed.

  4. Dimensional Crossover in Quantum Networks: From Macroscopic to Mesoscopic Physics

    NASA Astrophysics Data System (ADS)

    Schopfer, Félicien; Mallet, François; Mailly, Dominique; Texier, Christophe; Montambaux, Gilles; Bäuerle, Christopher; Saminadayar, Laurent

    2007-01-01

    We report on magnetoconductance measurements of metallic networks of various sizes ranging from 10 to 106 plaquettes, with an anisotropic aspect ratio. Both Altshuler-Aronov-Spivak h/2e periodic oscillations and Aharonov-Bohm h/e periodic oscillations are observed for all networks. For large samples, the amplitude of both oscillations results from the incoherent superposition of contributions of phase coherent regions. When the transverse size becomes smaller than the phase coherent length Lϕ, one enters a new regime which is phase coherent (mesoscopic) along one direction and macroscopic along the other, leading to a new size dependence of the quantum oscillations.

  5. Evaluation of Immunoassays and General Biological Indicator Tests for Field Screening of Bacillus anthracis and Ricin

    PubMed Central

    Bartholomew, Rachel A.; Ozanich, Richard M.; Arce, Jennifer S.; Engelmann, Heather E.; Heredia-Langner, Alejandro; Hofstad, Beth A.; Hutchison, Janine R.; Jarman, Kristin; Melville, Angela M.; Victry, Kristin D.

    2017-01-01

    There is little published data on the performance of biological indicator tests and immunoassays that could be used by first responders to determine if a suspicious powder contains a potential biothreat agent. We evaluated a range of biological indicator tests, including 3 protein tests, 2 ATP tests, 1 DNA test, and 1 FTIR spectroscopy instrument for their ability to screen suspicious powders for Bacillus anthracis (B. anthracis) spores and ricin. We also evaluated 12 immunoassays (mostly lateral flow immunoassays) for their ability to screen for B. anthracis and ricin. We used a cost-effective, statistically based test plan that allows instruments to be evaluated at performance levels ranging from 0.85 to 0.95 lower confidence bound of the probability of detection at confidence levels of 80% to 95%. We also assessed interference with 22 common suspicious powders encountered in the field. The detection reproducibility for the biological indicators was evaluated at 108 B. anthracis spores and 62.5 μg ricin, and the immunoassay detection reproducibility was evaluated at 107 spores/mL (B. anthracis) and 0.1 μg/mL (ricin). Seven out of 12 immunoassays met our most stringent criteria for B. anthracis detection, while 9 out of 12 met our most stringent test criteria for ricin detection. Most of the immunoassays also detected ricin in 3 different crude castor seed preparations. Our testing results varied across products and sample preparations, indicating the importance of reviewing performance data for specific instruments and sample types of interest for the application in order to make informed decisions regarding the selection of biodetection equipment for field use. PMID:28192054

  6. Science Teacher Efficacy and Outcome Expectancy as Predictors of Students' End-of-Instruction (EOI) Biology I Test Scores

    ERIC Educational Resources Information Center

    Angle, Julie; Moseley, Christine

    2009-01-01

    The purpose of this study was to compare teacher efficacy beliefs of secondary Biology I teachers whose students' mean scores on the statewide End-of-Instruction (EOI) Biology I test met or exceeded the state academic proficiency level (Proficient Group) to teacher efficacy beliefs of secondary Biology I teachers whose students' mean scores on the…

  7. SO-CALLED BIOLOGICAL TESTS FOR ADRENALIN IN BLOOD, WITH SOME OBSERVATIONS ON ARTERIAL HYPERTONUS

    PubMed Central

    Stewart, G. N.

    1911-01-01

    1. The combination of a biological test object on which adrenalin causes contraction of smooth muscle (perfused blood-vessels or the uterus in certain conditions) with a biological test object on which it produces inhibition of contraction of smooth muscle (intestine) greatly diminishes the chance of error in testing blood (or other body liquids) for adrenalin. A control experiment with adrenalin solutions should, in general, accompany each observation on the blood. 2. When properly chosen biological tests are employed, no evidence is obtained of the presence of adrenalin in detectable amount in normal blood taken from the general circulation. 3. In a case of nephritis with albuminuria and persistently high arterial pressure, the pressure was diminished by forced breathing. The washing out of carbon dioxide seemed to be a factor in this diminution as well as the mechanical interference with the circulation. In this case, the administration of large doses of sodium bicarbonate was associated with a marked diminution in the blood pressure. 4. In another case with persistently high blood pressure, the drawing off of cerebrospinal fluid caused a distinct diminution in the arterial pressure, presumably by lowering the intracranial pressure. No pressor substance was detected in the cerebrospinal fluid. PMID:19867483

  8. Development and testing of hyperbaric atomic force microscopy (AFM) and fluorescence microscopy for biological applications.

    PubMed

    D'Agostino, D P; McNally, H A; Dean, J B

    2012-05-01

    A commercially available atomic force microscopy and fluorescence microscope were installed and tested inside a custom-designed hyperbaric chamber to provide the capability to study the effects of hyperbaric gases on biological preparations, including cellular mechanism of oxidative stress. In this report, we list details of installing and testing atomic force microscopy and fluorescence microscopy inside a hyperbaric chamber. The pressure vessel was designed to accommodate a variety of imaging equipment and ensures full functionality at ambient and hyperbaric conditions (≤85 psi). Electrical, gas and fluid lines were installed to enable remote operation of instrumentation under hyperbaric conditions, and to maintain viable biological samples with gas-equilibrated superfusate and/or drugs. Systems were installed for vibration isolation and temperature regulation to maintain atomic force microscopy performance during compression and decompression. Results of atomic force microscopy testing demonstrate sub-nanometre resolution at hyperbaric pressure in dry scans and fluid scans, in both contact mode and tapping mode. Noise levels were less when measurements were taken under hyperbaric pressure with air, helium (He) and nitrogen (N(2) ). Atomic force microscopy and fluorescence microscopy measurements were made on a variety of living cell cultures exposed to hyperbaric gases (He, N(2) , O(2) , air). In summary, atomic force microscopy and fluorescence microscopy were installed and tested for use at hyperbaric pressures and enables the study of cellular and molecular effects of hyperbaric gases and pressure per se in biological preparations. © 2012 The Authors Journal of Microscopy © 2012 Royal Microscopical Society.

  9. Expertise for Teaching Biology Situated in the Context of Genetic Testing

    NASA Astrophysics Data System (ADS)

    Van der Zande, Paul; Akkerman, Sanne F.; Brekelmans, Mieke; Waarlo, Arend Jan; Vermunt, Jan D.

    2012-07-01

    Contemporary genomics research will impact the daily practice of biology teachers who want to teach up-to-date genetics in secondary education. This article reports on a research project aimed at enhancing biology teachers' expertise for teaching genetics situated in the context of genetic testing. The increasing body of scientific knowledge concerning genetic testing and the related consequences for decision-making indicate the societal relevance of an educational approach based on situated learning. What expertise do biology teachers need for teaching genetics in the personal health context of genetic testing? This article describes the required expertise by exploring the educational practice. Nine experienced teachers were interviewed about the pedagogical content, moral and interpersonal expertise areas concerning how to teach genetics in the personal health context of genetic testing, and the lessons of five of them were observed. The findings showed that the required teacher expertise encompasses specific pedagogical content expertise, interpersonal expertise and a preference for teacher roles and teaching approaches for the moral aspects of teaching in this context. A need for further development of teaching and learning activities for (reflection on) moral reasoning came to the fore. Suggestions regarding how to apply this expertise into context-based genetics education are discussed.

  10. Mesoscopic fluorescence tomography for in-vivo imaging of developing Drosophila.

    PubMed

    Vinegoni, Claudio; Razansky, Daniel; Pitsouli, Chrysoula; Perrimon, Norbert; Ntziachristos, Vasilis; Weissleder, Ralph

    2009-08-20

    Visualizing developing organ formation as well as progession and treatment of disease often heavily relies on the ability to optically interrogate molecular and functional changes in intact living organisms. Most existing optical imaging methods are inadequate for imaging at dimensions that lie between the penetration limits of modern optical microscopy (0.5-1mm) and the diffusion-imposed limits of optical macroscopy (>1cm) [1]. Thus, many important model organisms, e.g. insects, animal embryos or small animal extremities, remain inaccessible for in-vivo optical imaging. Although there is increasing interest towards the development of nanometer-resolution optical imaging methods, there have not been many successful efforts in improving the imaging penetration depth. The ability to perform in-vivo imaging beyond microscopy limits is in fact met with the difficulties associated with photon scattering present in tissues. Recent efforts to image entire embryos for example [2,3] require special chemical treatment of the specimen, to clear them from scattering, a procedure that makes them suitable only for post-mortem imaging. These methods however evidence the need for imaging larger specimens than the ones usually allowed by two-photon or confocal microscopy, especially in developmental biology and in drug discovery. We have developed a new optical imaging technique named Mesoscopic Fluorescence Tomography [4], which appropriate for non-invasive in-vivo imaging at dimensions of 1mm-5mm. The method exchanges resolution for penetration depth, but offers unprecedented tomographic imaging performance and it has been developed to add time as a new dimension in developmental biology observations (and possibly other areas of biological research) by imparting the ability to image the evolution of fluorescence-tagged responses over time. As such it can accelerate studies of morphological or functional dependencies on gene mutations or external stimuli, and can importantly

  11. Support for the revocation of general safety test regulations in biologics license applications.

    PubMed

    Evans, Dana M; Thorn, Jennifer M; Arch-Douglas, Katherine; Sperry, Justin B; Thompson, Bruce; Davis, Heather L; McCluskie, Michael J

    2016-05-01

    The United States Food and Drug Administration recently removed the requirement for a General Safety Test (GST) for biologics in the Code of Federal Regulations (21 CFR 610.11). The GST, as well as abnormal toxicity (European Pharmacopeia) and innocuity tests (World Health Organization), were designed to test for extraneous toxic contaminants on each product lot intended for human use. Tests require one-week observations for general health and weight following injection of specified volumes of product batches into guinea pigs and mice. At the volumes specified, dose-related toxicity may result when the product is pharmacologically active in rodents. With vaccines, required doses may be > 3 logs higher than intended human dose on a weight-adjusted basis and if an immune modulatory adjuvant is included, systemic immune hyperactivation may cause toxicity. Herein, using the CpG/alum adjuvant combination we evaluated the different test protocols and showed their unsuitability for this adjuvant combination.

  12. Modeling of mesoscopic electrokinetic phenomena using charged dissipative particle dynamics

    NASA Astrophysics Data System (ADS)

    Deng, Mingge; Li, Zhen; Karniadakis, George

    2015-11-01

    In this work, we propose a charged dissipative particle dynamics (cDPD) model for investigation of mesoscopic electrokinetic phenomena. In particular, this particle-based method was designed to simulate micro- or nano- flows which governing by Poisson-Nernst-Planck (PNP) equation coupled with Navier-Stokes (NS) equation. For cDPD simulations of wall-bounded fluid systems, a methodology for imposing correct Dirichlet and Neumann boundary conditions for both PNP and NS equations is developed. To validate the present cDPD model and the corresponding boundary method, we perform cDPD simulations of electrostatic double layer (EDL) in the vicinity of a charged wall, and the results show good agreement with the mean-field theoretical solutions. The capacity density of a parallel plate capacitor in salt solution is also investigated with different salt concentration. Moreover, we utilize the proposed methodology to study the electroosmotic and electroosmotic/pressure-driven flow in a micro-channel. In the last, we simulate the dilute polyelectrolyte solution both in bulk and micro-channel, which show the flexibility and capability of this method in studying complex fluids. This work was sponsored by the Collaboratory on Mathematics for Mesoscopic Modeling of Materials (CM4) supported by DOE.

  13. Mesoscopic Fluorescence Molecular Tomography for Evaluating Engineered Tissues

    PubMed Central

    Ozturk, Mehmet S.; Chen, Chao-Wei; Ji, Robin; Zhao, Lingling; Nguyen, Bao-Ngoc B.; Fisher, John P.; Chen, Yu; Intes, Xavier

    2015-01-01

    Optimization of regenerative medicine strategies includes the design of biomaterials, development of cell-seeding methods, and control of cell-biomaterial interactions within the engineered tissues. Among these steps, one paramount challenge is to non-destructively image the engineered tissues in their entirety to assess structure, function, and molecular expression. It is especially important to be able to enable cell phenotyping and monitor the distribution and migration of cells throughout the bulk scaffold. Advanced fluorescence microscopic techniques are commonly employed to perform such tasks; however, they are limited to superficial examination of tissue constructs. Therefore, the field of tissue engineering and regenerative medicine would greatly benefit from the development of molecular imaging techniques which are capable of non-destructive imaging of three-dimensional cellular distribution and maturation within a tissue-engineered scaffold beyond the limited depth of current microscopic techniques. In this review, we focus on an emerging depth-resolved optical mesoscopic imaging technique, termed Laminar Optical Tomography (LOT) or Mesoscopic Fluorescence Molecular Tomography (MFMT), which enables longitudinal imaging of cellular distribution in thick tissue engineering constructs at depths of a few millimeters and with relatively high resolution. The physical principle, image formation, and instrumentation of LOT/MFMT systems are introduced. Representative applications in tissue engineering include imaging the distribution of human mesenchymal stem cells (hMSCs) embedded in hydrogels, imaging of bio-printed tissues, and in vivo applications. PMID:26645079

  14. Assessment of mesoscopic particle-based methods in microfluidic geometries

    NASA Astrophysics Data System (ADS)

    Zhao, Tongyang; Wang, Xiaogong; Jiang, Lei; Larson, Ronald G.

    2013-08-01

    We assess the accuracy and efficiency of two particle-based mesoscopic simulation methods, namely, Dissipative Particle Dynamics (DPD) and Stochastic Rotation Dynamics (SRD) for predicting a complex flow in a microfluidic geometry. Since both DPD and SRD use soft or weakly interacting particles to carry momentum, both methods contain unavoidable inertial effects and unphysically high fluid compressibility. To assess these effects, we compare the predictions of DPD and SRD for both an exact Stokes-flow solution and nearly exact solutions at finite Reynolds numbers from the finite element method for flow in a straight channel with periodic slip boundary conditions. This flow represents a periodic electro-osmotic flow, which is a complex flow with an analytical solution for zero Reynolds number. We find that SRD is roughly ten-fold faster than DPD in predicting the flow field, with better accuracy at low Reynolds numbers. However, SRD has more severe problems with compressibility effects than does DPD, which limits the Reynolds numbers attainable in SRD to around 25-50, while DPD can achieve Re higher than this before compressibility effects become too large. However, since the SRD method runs much faster than DPD does, we can afford to enlarge the number of grid cells in SRD to reduce the fluid compressibility at high Reynolds number. Our simulations provide a method to estimate the range of conditions for which SRD or DPD is preferable for mesoscopic simulations.

  15. Mesoscopic aspects of phase transitions in a solvent extraction system.

    PubMed

    Ellis, Ross J; Audras, Matthieu; Antonio, Mark R

    2012-11-06

    In liquid-liquid extraction, organic phase splitting arises when high concentrations of polar solutes (acids/metal ions) are extracted. Herein, we investigate the mesoscopic roots that underpin phase splitting in alkane phases containing mixed amphiphiles, of contemporary interest in solvent extraction separation systems, by extracting various oxoacids. The oxoacids exhibited individual macroscopic (extractive and physical) behaviors, inducing phase splitting into heavy and light domains under markedly different conditions. Using small-angle X-ray scattering (SAXS) data analyzed using the generalized indirect Fourier transform (GIFT) method, we showed that, in all cases, acid extraction drove the self-assembly of reverse micelles into rods. These grew with increased acid extraction until reaching a critical length of 20 nm, at which point interactions produced interconnected cylinders or lamellar sheets that prelude phase splitting into heavy and light domains. In all cases, the heavy phase contained the same surfactant ratio-TBP (tri-n-butyl phosphate) and CMPO (octyl(phenyl)-N,N-diisobutylcarbamoylmethylphosphine oxide)-even though the concentrations of acid, water, and amphiphiles were markedly different. The remarkable similarities in structure and amphiphile stoichiometries underpinning phase splitting across the macroscopically different acid extraction series allude to the mesoscopic roots of organic phase behavior in solvent extraction. Our studies show that the structures underpinning phase splitting in solvent extraction systems are more complex than previously thought and are reminiscent of phase transitions in soft matter.

  16. Mesoscopic Dynamics of Biopolymers and Protein Molecular Machines

    NASA Astrophysics Data System (ADS)

    Kapral, Raymond

    2013-03-01

    The dynamics of biopolymers in solution and in crowded molecular environments, which mimic some features of the interior of a biochemical cell, will be discussed. In particular, the dynamics of protein machines that utilize chemical energy to effect cyclic conformational changes to carry out their catalytic functions will be described. The investigation of the dynamics of such complex systems requires knowledge of the time evolution on physically relevant long distance and time scales. This often necessitates a coarse grained or mesoscopic treatment of the dynamics. A hybrid particle-based mesoscopic dynamical method, which combines molecular dynamics for a coarse-grain model of the proteins with multiparticle collision dynamics for the solvent, will be described and utilized to study the dynamics of such systems. See, C. Echeverria, Y. Togashi, A. S. Mikhailov, and R. Kapral, Phys. Chem. Chem. Phys 13, 10527 (2011); C. Echeverria and R. Kapral, Phys. Chem. Chem. Phys., 14, 6755 (2012); J. M. Schofield, P. Inder and R. Kapral, J. Chem. Phys. 136, 205101 (2012). Work was supported in part by a grant from the Natural Sciences and Engineering Research Council of Canada.

  17. An effective mesoscopic model of double-stranded DNA.

    PubMed

    Jeon, Jae-Hyung; Sung, Wokyung

    2014-01-01

    Watson and Crick's epochal presentation of the double helix structure in 1953 has paved the way to intense exploration of DNA's vital functions in cells. Also, recent advances of single molecule techniques have made it possible to probe structures and mechanics of constrained DNA at length scales ranging from nanometers to microns. There have been a number of atomistic scale quantum chemical calculations or molecular level simulations, but they are too computationally demanding or analytically unfeasible to describe the DNA conformation and mechanics at mesoscopic levels. At micron scales, on the other hand, the wormlike chain model has been very instrumental in describing analytically the DNA mechanics but lacks certain molecular details that are essential in describing the hybridization, nano-scale confinement, and local denaturation. To fill this fundamental gap, we present a workable and predictive mesoscopic model of double-stranded DNA where the nucleotides beads constitute the basic degrees of freedom. With the inter-strand stacking given by an interaction between diagonally opposed monomers, the model explains with analytical simplicity the helix formation and produces a generalized wormlike chain model with the concomitant large bending modulus given in terms of the helical structure and stiffness. It also explains how the helical conformation undergoes overstretch transition to the ladder-like conformation at a force plateau, in agreement with the experiment.

  18. Fano interference in mesoscopic rings with quantum dots

    NASA Astrophysics Data System (ADS)

    Moldoveanu, V.; Aldea, A.; Olea, M.

    2006-02-01

    We propose a general formalism for describing the coexistence of coherent and resonant transport in hybrid mesoscopic structures. The approach is based on Landauer-Büttiker formula for the electronic transmittance and on an old formula of Feshbach. The latter gives the complete Green function of coupled subsystems in terms of effective Green functions of the disconnected parts and provides informations about the individual contributions of each subsystem to transport. Motivated by the experiments of Kobayashi et al.(Phys. Rev. Lett. 88, 256806 (2002)) and Holleitner et al. (Phys. Rev. Lett. 87, 256802 (2001)) we apply the formalism to study transport in Aharonov-Bohm interferometers (ABI) containing one or two coupled two-dimensional quantum dots (QD). In the single dot case, we reproduce and explain the magnetic field control of the Fano interference and investigate the interaction effects in a self-consistent approach. In the double dot case, we obtain the charging diagrams and establish precise criteria for the observation of mesoscopic Fano effect and AB oscillations.

  19. Mesoscopic fluctuations in biharmonically driven flux qubits

    NASA Astrophysics Data System (ADS)

    Ferrón, Alejandro; Domínguez, Daniel; Sánchez, María José

    2017-01-01

    We investigate flux qubits driven by a biharmonic magnetic signal, with a phase lag that acts as an effective time reversal broken parameter. The driving induced transition rate between the ground and the excited state of the flux qubit can be thought of as an effective transmittance, profiting from a direct analogy between interference effects at avoided level crossings and scattering events in disordered electronic systems. For time scales prior to full relaxation, but large compared to the decoherence time, this characteristic rate has been accessed experimentally by Gustavsson et al. [Phys. Rev. Lett. 110, 016603 (2013)], 10.1103/PhysRevLett.110.016603 and its sensitivity with both the phase lag and the dc flux detuning explored. In this way, signatures of universal conductance fluctuationslike effects have been analyzed and compared with predictions from a phenomenological model that only accounts for decoherence, as a classical noise. Here we go beyond the classical noise model and solve the full dynamics of the driven flux qubit in contact with a quantum bath employing the Floquet-Born-Markov master equation. Within this formalism, the computed relaxation and decoherence rates turn out to be strongly dependent on both the phase lag and the dc flux detuning. Consequently, the associated pattern of fluctuations in the characteristic rates display important differences with those obtained within the mentioned phenomenological model. In particular, we demonstrate the weak localizationlike effect in the average values of the relaxation rate. Our predictions can be tested for accessible but longer time scales than the current experimental times.

  20. Mycoplasma testing of cell substrates and biologics: Review of alternative non-microbiological techniques.

    PubMed

    Volokhov, Dmitriy V; Graham, Laurie J; Brorson, Kurt A; Chizhikov, Vladimir E

    2011-01-01

    Mycoplasmas, particularly species of the genera Mycoplasma and Acholeplasma, are known to be occasional microbial contaminants of cell cultures that produce biologics. This presents a serious concern regarding the risk of mycoplasma contamination for research laboratories and commercial facilities developing and manufacturing cell-derived biological and biopharmaceutical products for therapeutic use. Potential undetected contamination of these products or process intermediates with mycoplasmas represents a potential safety risk for patients and a business risk for producers of biopharmaceuticals. To minimize these risks, monitoring for adventitious agents, such as viruses and mycoplasmas, is performed during the manufacture of biologics produced in cell culture substrates. The "gold standard" microbiological assay, currently recommended by the USP, EP, JP and the US FDA, for the mycoplasma testing of biologics, involves the culture of viable mycoplasmas in broth, agar plates and indicator cells. Although the procedure enables highly efficient mycoplasma detection in cell substrates and cell-derived products, the overall testing strategy is time consuming (a minimum of 28 days) and requires skilled interpretation of the results. The long time period required for these conventional assays does not permit their use for products with short shelf-lives or for timely 'go/no-go' decisions during routine in-process testing. PCR methodology has existed for decades, however PCR based and other alternative methods for mycoplasma detection have only recently been considered for application to biologics manufacture. The application of alternative nucleic acid-based, enzyme-based and/or recombinant cell-culture methods, particularly in combination with efficient sample preparation procedures, could provide advantages over conventional microbiological methods in terms of analytical throughput, simplicity, and turnaround time. However, a challenge to the application of alternative

  1. Phosphorus recycling potential assessment by a biological test applied to wastewater sludge.

    PubMed

    Braak, Etienne; Auby, Sarah; Piveteau, Simon; Guilayn, Felipe; Daumer, Marie-Line

    2016-01-01

    Phosphorus (P) recycling as mineral fertilizer from wastewater activated sludge (WAS) depends on the amount that can be dissolved and separated from the organic matter before the final crystallization step. The aim of the biological phosphorus dissolution potential (BPDP) test developed here was to assess the maximum amount of P that could be biologically released from WAS prior that the liquid phase enters the recovery process. It was first developed for sludge combining enhanced biological phosphorus removal and iron chloride. Because carbohydrates are known to induce acidification during the first stage of anaerobic digestion, sucrose was used as a co-substrate. Best results were obtained after 24-48 h, without inoculum, with a sugar/sludge ratio of 0.5 gCOD/gVS and under strict anaerobic conditions. Up to 75% of the total phosphorus in sludge from a wastewater treatment plant combining enhanced biological phosphorus removal and iron chloride phosphorus removal could be dissolved. Finally, the test was applied to assess BPDP from different sludge using alum compounds for P removal. No dissolution was observed when alum polychloride was used and less than 20% when alum sulphate was used. In all the cases, comparison to chemical acidification showed that the biological process was a major contributor to P dissolution. The possibility to crystallize struvite was discussed from the composition of the liquids obtained. The BPDP will be used not only to assess the potential for phosphorus recycling from sludge, but also to study the influence of the co-substrates available for anaerobic digestion of sludge.

  2. Unconventional states and geometric effects in mesoscopic systems of ultra-cold atomic Fermi gases

    SciTech Connect

    Bolech, C. J.

    2014-10-15

    During the last decade, experiments all over the world started to test the superconducting state of matter using a newly developed mesoscopic tunable system: trapped ultra-cold atomic gases. Theorists and experimentalists hand-in-hand are now able to advance our understanding of the superconducting state by asking new questions that probe further into the physical mechanisms underlying the phenomenon and the door is open to the exploration of exotic unconventional superconducting states. In particular, a series of experiments on systems of trapped cold atomic gases were aimed at studying the effects of polarization on superconducting pairing. Two different experimental groups encountered surprising qualitative and quantitative discrepancies which seemed to be a function of the confining geometry and the cooling protocol. Our numerical studies demonstrate a tendency towards metastability and suggest an explanation for the observed discrepancy. From our calculations, the most likely solution which is consistent with the experiments supports a state strikingly similar to the so called FFLO state (after Ferrell, Fulde, Larkin and Ovchinnikov), which had been theorized long ago but eluded detection so far. Moreover, the three-dimensional scenario described above is reminiscent of predictions for one-dimensional systems of dilute polarized attractive gases and another set of ultra-cold-atom experiments incorporates optical lattices to study this reduced-dimensionality setting. The measurements are in quantitative agreement with theoretical calculations (using a wide array of numerical and analytic techniques) in which a partially polarized phase is found to be the one-dimensional analogue of the FFLO state. Moreover, exploring the dimensional-crossover regime, our latest findings indicate that the mesoscopic nature of these quasi-one-dimensional systems favors the appearance of a new type of Mott phase transition involving an emergent pair-superfluid of equal

  3. Seismoelectric signals produced by mesoscopic heterogeneities: an analytical and numerical study

    NASA Astrophysics Data System (ADS)

    Linde, N.; Rosas Carbajal, M.; Rubino, J. G.; Monachesi, L. B.; Jougnot, D.; Holliger, K.

    2014-12-01

    The presence of mesoscopic heterogeneities, such as fractures, in fluid-saturated porous rocks can produce measurable seismoelectric signals due to wave-induced fluid flow between regions of differing compressibility. Wave-induced fluid flow is a well-known seismic attenuation mechanism, which evidences a strong frequency-dependence that is related to petrophysical and structural properties of the host rock. Therefore, seismoelectric signals arising from this mechanism are expected to depend on the same kind of parameters. However, these remain largely unexplored. In this work, we first propose a numerical approach for computing seismoelectric signals related to the presence of mesoscopic heterogeneities and explore its spectroscopic behavior. To obtain the explicit dependence of the seismoelectric signal on petrophysical and structural parameters, we derive an analytical solution to describe the seismoelectric response of a rock sample containing a horizontal layer at its center that is subjected to an oscillatory compressibility test. We then adapt this general solution to compute the seismoelectric signature of a particular case related to a sample that is permeated by a horizontal fracture. We find that the amplitude of the seismoelectric signal is directly proportional to the applied stress, to the Skempton coefficient contrast between the host rock and the layer, and to a weighted average of the effective excess charge of the two materials. Our results also demonstrate that the frequency at which the maximum electrical potential amplitude prevails is controlled by the permeability and thickness of the less permeable material. The results of this study thus indicate that seismoelectric measurements can potentially be used to estimate key mechanical and hydraulic rock properties, such as compressibility, permeability, and fracture normal compliance.

  4. Sound and faulty arguments generated by preservice biology teachers when testing hypotheses involving unobservable entities

    NASA Astrophysics Data System (ADS)

    Lawson, Anton E.

    2002-03-01

    A sample of preservice biology teachers (biology majors) enrolled in a teaching methods course formulated and attempted to test six hypotheses to answer a causal question about why water rose in a jar inverted over a burning candle placed in a pan of water. The students submitted a lab report in which arguments and evidence for testing each hypothesis were presented in an if/then/therefore hypothetico-predictive form. Analysis of written arguments revealed considerable success when students were able to manipulate observable hypothesized causes. However, when the hypothesized causes were unobservable, such that they could be only indirectly tested, performance dropped, as shown by use of three types of faulty arguments: (a) arguments that had missing or confused elements, (b) arguments whose predictions did not follow from hypotheses and planned tests, and (c) arguments that failed to consider alternative hypotheses. Science is an enterprise in which unobservable theoretical entities and processes (e.g., atoms, genes, osmosis, and photosynthesis) are often used to explain observable phenomena. Consequently, if it is assumed that effective teaching requires prior understanding, then it follows that these future teachers have yet to develop adequate hypothesis-testing skills and sufficient awareness of the nature of science to teach science in the inquiry mode advocated by reform guidelines.

  5. "Active" drops as phantom models for living cells: a mesoscopic particle-based approach.

    PubMed

    Dallavalle, Marco; Lugli, Francesca; Rapino, Stefania; Zerbetto, Francesco

    2016-04-21

    Drops and biological cells share some morphological features and visco-elastic properties. The modelling of drops by mesoscopic non-atomistic models has been carried out to a high degree of success in recent years. We extend such treatment and discuss a simple, drop-like model to describe the interactions of the outer layer of cells with the surfaces of materials. Cells are treated as active mechanical objects that are able to generate adhesion forces. They appear with their true size and are made of "parcels of fluids" or beads. The beads are described by (very) few quantities/parameters related to fundamental chemical forces such as hydrophilicity and lipophilicity that represent an average of the properties of a patch of material or an area of the cell(s) surface. The investigation of adhesion dynamics, motion of individual cells, and the collective behavior of clusters of cells on materials is possible. In the simulations, the drops become active soft matter objects and different from regular droplets they do not fuse when in contact, their trajectories are not Brownian, and they can be forced "to secrete" molecules, to name some of the properties targeted by the modeling. The behavior that emerges from the simulations allows ascribing some cell properties to their mechanics, which are related to their biological features.

  6. Time dependence of mesoscopic strain distribution for triaxial woven carbon-fiber-reinforced polymer under creep loading measured by digital image correlation

    NASA Astrophysics Data System (ADS)

    Koyanagi, Jun; Nagayama, Hideo; Yoneyama, Satoru; Aoki, Takahira

    2016-06-01

    This paper presents the time dependence of the mesoscopic strain of a triaxial woven carbon-fiber-reinforced polymer under creep loading measured using digital image correlation (DIC). Two types of DIC techniques were employed for the measurement: conventional subset DIC and mesh DIC. Static tensile and creep tests were carried out, and the time dependence of the mesoscopic strain distribution was investigated by applying these techniques. The ultimate failure of this material is dominated by inter-bundle decohesion caused by relative rigid rotation and relating shear stress. Therefore, these were focused on in the present study. During the creep tests, the fiber directional strain, shear strain, and rotation were monitored using the DIC, and the mechanism for the increase in the specimen's macro-strain over time was investigated based on the results obtained by the DIC measurement.

  7. Insects as test systems for assessing the potential role of microgravity in biological development and evolution

    NASA Astrophysics Data System (ADS)

    Vernós, I.; Carratalá, M.; González-Jurado, J.; Valverde, J. R.; Calleja, M.; Domingo, A.; Vinós, J.; Cervera, M.; Marco, R.

    Gravity and radiation are undoubtedly the two major environmental factors altered in space. Gravity is a weak force, which creates a permanent potential field acting on the mass of biological systems and their cellular components, strongly reduced in space flights. Developmental systems, particularly at very early stages, provide the larger cellular compartments known, where the effects of alterations in the size of the gravity vector on living organisms can be more effectively tested. The insects, one of the more highly evolved classes of animals in which early development occurs in a syncytial embryo, are systems particularly well suited to test these effects and the specific developmental mechanisms affected. Furthermore, they share some basic features such as small size, short life cycles, relatively high radio-resistance, etc. and show a diversity of developmental strategies and tempos advantageous in experiments of this type in space. Drosophila melanogaster, the current biological paradigm to study development, with so much genetic and evolutionary background available, is clearly the reference organism for these studies. The current evidence on the effects of the physical parameters altered in space flights on insect development indicate a surprising correlation between effects seen on the fast developing and relatively small Drosophila embryo and the more slowly developing and large Carausius morosus system. In relation to the issue of the importance of developmental and environmental constraints in biological evolution, still the missing link in current evolutionary thinking, insects and space facilities for long-term experiments could provide useful experimental settings where to critically assess how development and evolution may be interconnected. Finally, it has to be pointed out that since there are experimental data indicating a possible synergism between microgravity and space radiation, possible effects of space radiation should be taken into

  8. Insects as test systems for assessing the potential role of microgravity in biological development and evolution.

    PubMed

    Vernós, I; Carratalá, M; González-Jurado, J; Valverde, J R; Calleja, M; Domingo, A; Vinós, J; Cervera, M; Marco, R

    1989-01-01

    Gravity and radiation are undoubtedly the two major environmental factors altered in space. Gravity is a weak force, which creates a permanent potential field acting on the mass of biological systems and their cellular components, strongly reduced in space flights. Developmental systems, particularly at very early stages, provide the larger cellular compartments known, where the effects of alterations in the size of the gravity vector on living organisms can be more effectively tested. The insects, one of the more highly evolved classes of animals in which early development occurs in a syncytial embryo, are systems particularly well suited to test these effects and the specific developmental mechanisms affected. Furthermore, they share some basic features such as small size, short life cycles, relatively high radio-resistance, etc. and show a diversity of developmental strategies and tempos advantageous in experiments of this type in space. Drosophila melanogaster, the current biological paradigm to study development, with so much genetic and evolutionary background available, is clearly the reference organism for these studies. The current evidence on the effects of the physical parameters altered in space flights on insect development indicate a surprising correlation between effects seen on the fast developing and relatively small Drosophila embryo and the more slowly developing and large Carausius morosus system. In relation to the issue of the importance of developmental and environmental constraints in biological evolution, still the missing link in current evolutionary thinking, insects and space facilities for long-term experiments could provide useful experimental settings where to critically assess how development and evolution may be interconnected. Finally, it has to be pointed out that since there are experimental data indicating a possible synergism between microgravity and space radiation, possible effects of space radiation should be taken into

  9. DAISY: a new software tool to test global identifiability of biological and physiological systems.

    PubMed

    Bellu, Giuseppina; Saccomani, Maria Pia; Audoly, Stefania; D'Angiò, Leontina

    2007-10-01

    A priori global identifiability is a structural property of biological and physiological models. It is considered a prerequisite for well-posed estimation, since it concerns the possibility of recovering uniquely the unknown model parameters from measured input-output data, under ideal conditions (noise-free observations and error-free model structure). Of course, determining if the parameters can be uniquely recovered from observed data is essential before investing resources, time and effort in performing actual biomedical experiments. Many interesting biological models are nonlinear but identifiability analysis for nonlinear system turns out to be a difficult mathematical problem. Different methods have been proposed in the literature to test identifiability of nonlinear models but, to the best of our knowledge, so far no software tools have been proposed for automatically checking identifiability of nonlinear models. In this paper, we describe a software tool implementing a differential algebra algorithm to perform parameter identifiability analysis for (linear and) nonlinear dynamic models described by polynomial or rational equations. Our goal is to provide the biological investigator a completely automatized software, requiring minimum prior knowledge of mathematical modelling and no in-depth understanding of the mathematical tools. The DAISY (Differential Algebra for Identifiability of SYstems) software will potentially be useful in biological modelling studies, especially in physiology and clinical medicine, where research experiments are particularly expensive and/or difficult to perform. Practical examples of use of the software tool DAISY are presented. DAISY is available at the web site http://www.dei.unipd.it/~pia/.

  10. Testing for phylogenetic signal in biological traits: the ubiquity of cross-product statistics.

    PubMed

    Pavoine, Sandrine; Ricotta, Carlo

    2013-03-01

    To evaluate rates of evolution, to establish tests of correlation between two traits, or to investigate to what degree the phylogeny of a species assemblage is predictive of a trait value so-called tests for phylogenetic signal are used. Being based on different approaches, these tests are generally thought to possess quite different statistical performances. In this article, we show that the Blomberg et al. K and K*, the Abouheif index, the Moran's I, and the Mantel correlation are all based on a cross-product statistic, and are thus all related to each other when they are associated to a permutation test of phylogenetic signal. What changes is only the way phylogenetic and trait similarities (or dissimilarities) among the tips of a phylogeny are computed. The definitions of the phylogenetic and trait-based (dis)similarities among tips thus determines the performance of the tests. We shortly discuss the biological and statistical consequences (in terms of power and type I error of the tests) of the observed relatedness among the statistics that allow tests for phylogenetic signal. Blomberg et al. K* statistic appears as one on the most efficient approaches to test for phylogenetic signal. When branch lengths are not available or not accurate, Abouheif's Cmean statistic is a powerful alternative to K*.

  11. Biological variability of the sweat chloride in diagnostic sweat tests: A retrospective analysis.

    PubMed

    Vermeulen, F; Lebecque, P; De Boeck, K; Leal, T

    2017-01-01

    The sweat test is the current gold standard for the diagnosis of cystic fibrosis (CF). CF is unlikely when sweat chloride (Clsw) is lower than 30mmol/L, Clsw>60 is suggestive of CF, with intermediate values between 30 and 60mmol/L. To correctly interpret a sweat chloride value, the biological variability of the sweat chloride has to be known. Sweat tests performed in two centers using the classic Gibson and Cooke method were retrospectively reviewed (n=5904). Within test variability of Clsw was measured by comparing results from right and left arm collected on the same day. Between test variability was calculated from subjects with sweat tests performed on more than one occasion. Within test variability of Clsw calculated in 1022 subjects was low with differences between -3.2 (p5) and +3.6mmol/L (p95). Results from left and right arm were classified differently in only 3 subjects. Between test variability of Clsw in 197 subjects was larger, with differences between -18.2mmol/L (p5) and +14.1mmol/L (p95) between repeat tests. Changes in diagnostic conclusion were seen in 55/197 subjects, the most frequent being changing from indeterminate to 'CF unlikely' range (48/102). Variability of sweat chloride is substantial, with frequent changes in diagnostic conclusion, especially in the intermediate range. Copyright © 2016 European Cystic Fibrosis Society. Published by Elsevier B.V. All rights reserved.

  12. Detecting Change in Biological Rhythms: A Multivariate Permutation Test Approach to Fourier-Transformed Data

    PubMed Central

    Blackford, Jennifer Urbano; Salomon, Ronald M.; Waller, Niels G.

    2009-01-01

    Treatment-related changes in neurobiological rhythms are of increasing interest to psychologists, psychiatrists, and biological rhythms researchers. New methods for analyzing change in rhythms are needed, as most common methods disregard the rich complexity of biological processes. Large time series data sets reflect the intricacies of underlying neurobiological processes, but can be difficult to analyze. We propose the use of Fourier methods with multivariate permutation test (MPT) methods for analyzing change in rhythms from time series data. To validate the use of MPT for Fourier-transformed data, we performed Monte Carlo simulations and compared statistical power and family-wise error for MPT to Bonferroni-corrected and uncorrected methods. Results show that MPT provides greater statistical power than Bonferroni-corrected tests, while appropriately controlling family-wise error. We applied this method to human, pre-and post-treatment, serially-sampled neurotransmitter data to confirm the utility of this method using real data. Together, Fourier with MPT methods provides a statistically powerful approach for detecting change in biological rhythms from time series data. PMID:19212840

  13. Computational systems biology and dose-response modeling in relation to new directions in toxicity testing.

    PubMed

    Zhang, Qiang; Bhattacharya, Sudin; Andersen, Melvin E; Conolly, Rory B

    2010-02-01

    The new paradigm envisioned for toxicity testing in the 21st century advocates shifting from the current animal-based testing process to a combination of in vitro cell-based studies, high-throughput techniques, and in silico modeling. A strategic component of the vision is the adoption of the systems biology approach to acquire, analyze, and interpret toxicity pathway data. As key toxicity pathways are identified and their wiring details elucidated using traditional and high-throughput techniques, there is a pressing need to understand their qualitative and quantitative behaviors in response to perturbation by both physiological signals and exogenous stressors. The complexity of these molecular networks makes the task of understanding cellular responses merely by human intuition challenging, if not impossible. This process can be aided by mathematical modeling and computer simulation of the networks and their dynamic behaviors. A number of theoretical frameworks were developed in the last century for understanding dynamical systems in science and engineering disciplines. These frameworks, which include metabolic control analysis, biochemical systems theory, nonlinear dynamics, and control theory, can greatly facilitate the process of organizing, analyzing, and understanding toxicity pathways. Such analysis will require a comprehensive examination of the dynamic properties of "network motifs"--the basic building blocks of molecular circuits. Network motifs like feedback and feedforward loops appear repeatedly in various molecular circuits across cell types and enable vital cellular functions like homeostasis, all-or-none response, memory, and biological rhythm. These functional motifs and associated qualitative and quantitative properties are the predominant source of nonlinearities observed in cellular dose response data. Complex response behaviors can arise from toxicity pathways built upon combinations of network motifs. While the field of computational cell

  14. Methods for using 3-D ultrasound speckle tracking in biaxial mechanical testing of biological tissue samples.

    PubMed

    Yap, Choon Hwai; Park, Dae Woo; Dutta, Debaditya; Simon, Marc; Kim, Kang

    2015-04-01

    Being multilayered and anisotropic, biological tissues such as cardiac and arterial walls are structurally complex, making the full assessment and understanding of their mechanical behavior challenging. Current standard mechanical testing uses surface markers to track tissue deformations and does not provide deformation data below the surface. In the study described here, we found that combining mechanical testing with 3-D ultrasound speckle tracking could overcome this limitation. Rat myocardium was tested with a biaxial tester and was concurrently scanned with high-frequency ultrasound in three dimensions. The strain energy function was computed from stresses and strains using an iterative non-linear curve-fitting algorithm. Because the strain energy function consists of terms for the base matrix and for embedded fibers, spatially varying fiber orientation was also computed by curve fitting. Using finite-element simulations, we first validated the accuracy of the non-linear curve-fitting algorithm. Next, we compared experimentally measured rat myocardium strain energy function values with those in the literature and found a matching order of magnitude. Finally, we retained samples after the experiments for fiber orientation quantification using histology and found that the results satisfactorily matched those computed in the experiments. We conclude that 3-D ultrasound speckle tracking can be a useful addition to traditional mechanical testing of biological tissues and may provide the benefit of enabling fiber orientation computation.

  15. Review: production, characterization, and testing of banked mammalian cell substrates used to produce biological products.

    PubMed

    Schiff, Leonard J

    2005-01-01

    A critical component in controlling the production of biological products derived from human and animal cell lines is the characterization and testing of banked cell substrates. The objective is to confirm the identity, purity, and suitability of these cells for manufacturing use. Quality concerns for biological products derived from cell lines originate from the presence of cellular and adventitious contaminants. Well-characterized cell banks not only permit a consistent source of production cells throughout the life of a product but also decrease the likelihood of contamination by other cell lines and adventitious agents. An important part of qualifying a cell line is choosing the appropriate testing for the presence of adventitious contaminants. The qualification of cell banks includes tests for cell identity and endogenous and adventitious microbial contaminants (bacteria, fungi, mycoplasmas, and viruses). For cells producing recombinant deoxyribonucleic acid-derived products, analysis of the expression construct at the nucleic acid level (genetic stability) is also a primary concern. The strategy for designing a safety-testing program for banked cells should be based on sound scientific principles and current regulatory guidance.

  16. METHODS FOR USING 3-D ULTRASOUND SPECKLE TRACKING IN BIAXIAL MECHANICAL TESTING OF BIOLOGICAL TISSUE SAMPLES

    PubMed Central

    Yap, Choon Hwai; Park, Dae Woo; Dutta, Debaditya; Simon, Marc; Kim, Kang

    2014-01-01

    Being multilayered and anisotropic, biological tissues such as cardiac and arterial walls are structurally complex, making full assessment and understanding of their mechanical behavior challenging. Current standard mechanical testing uses surface markers to track tissue deformations and does not provide deformation data below the surface. In the study described here, we found that combining mechanical testing with 3-D ultrasound speckle tracking could overcome this limitation. Rat myocardium was tested with a biaxial tester and was concurrently scanned with high-frequency ultrasound in three dimensions. The strain energy function was computed from stresses and strains using an iterative non-linear curve-fitting algorithm. Because the strain energy function consists of terms for the base matrix and for embedded fibers, spatially varying fiber orientation was also computed by curve fitting. Using finite-element simulations, we first validated the accuracy of the non-linear curve-fitting algorithm. Next, we compared experimentally measured rat myocardium strain energy function values with those in the literature and found a matching order of magnitude. Finally, we retained samples after the experiments for fiber orientation quantification using histology and found that the results satisfactorily matched those computed in the experiments. We conclude that 3-D ultrasound speckle tracking can be a useful addition to traditional mechanical testing of biological tissues and may provide the benefit of enabling fiber orientation computation. PMID:25616585

  17. HRI catalytic two-stage liquefaction (CTSL) process materials: chemical analysis and biological testing

    SciTech Connect

    Wright, C.W.; Later, D.W.

    1985-12-01

    This report presents data from the chemical analysis and biological testing of coal liquefaction materials obtained from the Hydrocarbon Research, Incorporated (HRI) catalytic two-stage liquefaction (CTSL) process. Materials from both an experimental run and a 25-day demonstration run were analyzed. Chemical methods of analysis included adsorption column chromatography, high-resolution gas chromatography, gas chromatography/mass spectrometry, low-voltage probe-inlet mass spectrometry, and proton nuclear magnetic resonance spectroscopy. The biological activity was evaluated using the standard microbial mutagenicity assay and an initiation/promotion assay for mouse-skin tumorigenicity. Where applicable, the results obtained from the analyses of the CTSL materials have been compared to those obtained from the integrated and nonintegrated two-stage coal liquefaction processes. 18 refs., 26 figs., 22 tabs.

  18. The conversion rate of tuberculosis screening tests during biological therapies in patients with rheumatoid arthritis.

    PubMed

    Cuomo, Giovanna; D'Abrsca, Virginia; Iacono, Daniela; Pantano, Ilenia

    2017-02-01

    Screening for active tuberculosis (TB) and latent TB infection (LTBI) is mandatory to the initiation of biological therapy in patients with rheumatic diseases. To determine the prevalence of LTBI in patients with rheumatoid arthritis before treatment with biological therapy (anti-TNF, abatacept, and tocilizumab) and the rate of TB conversion during treatment in rheumatoid arthritis (RA) patients, we evaluated the file of 275 patients with RA treated with biological agents. We considered patients with negative baseline TB screening (tuberculin skin test (TST); quantiferon TB gold in tube (QFT-GIT); chest x-ray) and with rescreening for a TB assay every year. Twenty-six patients (10.6%) resulted positive to TB screening at baseline. Two hundred and forty-nine patients (mean age 55.3 ± 11.9; median 55.8 years, range 16-81.9; 210 female) with TB screening negative at baseline were enrolled. One hundred and sixty-eight (67.5%) patients were treated with anti-TNF, 37 (14.9%) patients with abatacept, and 44 (17.7%) patients with tocilizumab. After a period of 12-120 months (median 24), 34 (13.6%) patients displayed conversion of at least one screening assay. Out of the 34 patients with conversion, 6 (16.2%) were treated with abatacept, 7 (15.9%) with tocilizumab, and 21 (12.5%) with anti-TNF. During the follow-up period, no patients developed active TB. Our study shows that a proportion of patients (13.6%) converts at least one TB screening assay during biological therapy. This study underscores the American College of Rheumatology advice for annual screening in some or all biologically treated patients.

  19. An experimental test of an extended discretion approach for high school biology laboratory investigations

    NASA Astrophysics Data System (ADS)

    Leonard, William H.; Cavana, Gordon R.; Lowery, Lawrence F.

    Discretion-the exercise of independent judgment-was observed to be lacking in most commercially available laboratory investigations for high school biology. An Extended Discretion (ED) laboratory approach was developed and tested experimentally against the BSCS Green Version laboratory program, using ten classes of 10th-grade biology in a suburban California high school. Five teachers were each assigned one experimental and one control group. The primary differences between the two approaches were that the BSCS was more prescriptive and directive than the ED approach and the ED approach increased discretionary demands upon the student over the school year. A treatment verification procedure showed statistically significant differences between the two approaches. The hypothesis under test was that when high school biology students are taught laboratory concepts under comparatively high discretionary demands, they would perform as well as or better than a similar group of students taught with BSCS Green Version investigations. A second hypothesis was that teachers would prefer to use the ED approach over the BSCS approach for their future classes. A t analysis between experimental and control groups for each teacher was employed. There were significant differences in favor of the ED group on laboratory report scores for three teachers and no differences for two teachers. There were significant differences in favor of the ED group on laboratory concepts quiz scores for three teachers, no differences for one teacher, and significant differences in favor of the BSCS group for only one teacher. A t analysis of teacher evaluation of the two approaches showed a significant teacher preference overall for the ED approach. Both experimental hypotheses were accepted. The ED approach was observed to be difficult for students at first, but it was found to be a workable and productive means of teaching laboratory concepts in biology which also required extensive use of individual

  20. [Plasma antioxidant activity--a test for impaired biological functions of endoecology, exotrophy, and inflammation reactions].

    PubMed

    Titov, V N; Krylin, V V; Dmitriev, V A; Iashin, Ia I

    2010-07-01

    The authors discuss the diagnostic value of a test for total serum antioxidant activity determined by an electrochemistry method on a liquid chromatograph (without a column), by using an amperometric detector, as well as the composition of the endogenously synthesized hydrophilic and hydrophobic acceptors of reactive oxygen species (ROS). Uric acid is a major hydrophilic acceptor of ROS; monoenic oleic fatty acid acts as its major lipophilic acceptor. The constant determined by the authors for of 03 oleic acid oxidation during automatic titration in the organic medium is an order of magnitude higher than that for alpha-tocopherol, beta-carotene and linoleic fatty acid; its concentration is also an order of magnitude higher. In oxidative stress, the adrenal steroid hormone dehydroepiandrosterone initiates oleic acid synthesis via expression of palmitoyl elongase and steatoryl desaturase. In early steps of phylogenesis in primates, spontaneous mutation resulted in ascorbic acid synthesis gene knockout; phylogenetically, further other mutation knocked out the gene encoding the synthesis of uricase and the conversion of uric acid to alantoin. In primates, uric acid became not only a catabolite of purine bases in vivo, but also the major endogenous hydrophilic acceptor of ROS. This philogenetic order makes it clear why the epithelium in the proximal nephron tubule entirely reabsorbs uric acid (a catabolite?) from primary urine and then secretes it again to urine depending on the impairment of biological functions of endoecology (the intercellular medium being contaminated with biological rubbish), the activation of a biological inflammatory reaction, the cellular production of ROS, and the reduction in serum total antioxidant activity. With each biological reaction, there was an increase in the blood content of uric acid as a hydrophilic acceptor of ROS, by actively lowering its secretion into urine. Uric acid is a diagnostic test of inflammation, or rather compensatory

  1. Interactions between electrons, mesoscopic Josephson effect and asymmetric current fluctuations

    NASA Astrophysics Data System (ADS)

    Huard, B.

    2006-07-01

    This article discusses three experiments on the properties of electronic transport at the mesoscopic scale. The first one allowed to measure the energy exchange rate between electrons in a metal contaminated by a very weak concentration of magnetic impurities. The role played by magnetic impurities in the Kondo regime on those energy exchanges is quantitatively investigated, and the global measured exchange rate is larger than expected. The second experiment is a measurement of the current-phase relation in a system made of two superconductors linked through a single atom. We thus provide quantitative support for the recent description of the mesoscopic Josephson effect. The last experiment is a measurement of the asymmetry of the current fluctuations in a mesoscopic conductor, using a Josephson junction as a threshold detector. Cet ouvrage décrit trois expériences portant sur les propriétés du transport électronique à l'échelle mésoscopique. La première a permis de mesurer le taux d'échange d'énergie entre électrons dans un métal contenant une très faible concentration d'impuretés magnétiques. Nous avons validé la description quantitative du rôle des impuretés magnétiques dans le régime Kondo sur ces échanges énergétiques et aussi montré que le taux global d'échange est plus fort que prévu. La seconde expérience est une mesure de la relation courant-phase dans un système constitué de deux supraconducteurs couplés par un seul atome. Elle nous a permis de conforter quantitativement la récente description de l'effet Josephson mésoscopique. La dernière expérience est unemesure de l'asymétrie des fluctuations du courant dans un conducteur mésoscopique en utilisant une Jonction Josephson comme détecteur de seuil.

  2. Inquiry-based laboratory investigations and student performance on standardized tests in biological science

    NASA Astrophysics Data System (ADS)

    Patke, Usha

    Achievement data from the 3rd International Mathematics and Sciences Study and Program for International Student Assessment in science have indicated that Black students from economically disadvantaged families underachieve at alarming rates in comparison to White and economically advantaged peer groups. The study site was a predominately Black, urban school district experiencing underachievement. The purpose of this correlational study was to examine the relationship between students' use of inquiry-based laboratory investigations and their performance on the Biology End of Course Test, as well as to examine the relationship while partialling out the effects of student gender. Constructivist theory formed the theoretical foundation of the study. Students' perceived levels of experience with inquiry-based laboratory investigations were measured using the Laboratory Program Variable Inventory (LPVI) survey. LPVI scores of 256 students were correlated with test scores and were examined by student gender. The Pearson correlation coefficient revealed a small direct correlation between students' experience in inquiry-based laboratory investigation classes and standardized test scores on the Biology EOCT. A partial correlational analysis indicated that the correlation remained after controlling for gender. This study may prompt a change from teacher-centered to student-centered pedagogy at the local site in order to increase academic achievement for all students. The results of this study may also influence administrators and policy makers to initiate local, state, or nationwide curricular development. A change in curriculum may promote social change as students become more competent, and more able, to succeed in life beyond secondary school.

  3. Mesoscopic Josephson junctions with switchable current-phase relation

    NASA Astrophysics Data System (ADS)

    Strambini, E.; Bergeret, F. S.; Giazotto, F.

    2015-10-01

    We propose and analyze a mesoscopic Josephson junction consisting of two ferromagnetic insulator-superconductors (FI-Ss) coupled through a normal metal (N) layer. The Josephson current of the junction is non-trivially affected by the spin-splitting field induced by the FIs in the two superconductors. In particular, it shows sizeable enhancement by increasing the amplitude of the exchange field (hex) and displays a switchable current-phase relation which depends on the relative orientation of h ex in the FIs. In a realistic EuS/Al-based setup this junction can be exploited as a high-resolution threshold sensor for the magnetic field as well as an on-demand tunable kinetic inductor.

  4. Spin accumulation on a one-dimensional mesoscopic Rashba ring.

    PubMed

    Zhang, Zhi-Yong

    2006-04-26

    The nonequilibrium spin accumulation on a one-dimensional (1D) mesoscopic Rashba ring is investigated with unpolarized current injected through ideal leads. Due to the Rashba spin-orbit (SO) coupling and back-scattering at the interfaces between the leads and the ring, a beating pattern is formed in the fast oscillation of spin accumulation. If every beating period is complete, a plateau is formed, where the variation of spin accumulation with the external voltage is slow, but if new incomplete periods emerge in the envelope function, a transitional region appears. This plateau structure and the beating pattern are related to the tunnelling through spin-dependent resonant states. Because of the Aharonov-Casher (AC) effect, the average spin accumulation oscillates quasi-periodically with the Rashba SO coupling and has a series of zeros. In some situations, the direction of the average spin accumulation can be reversed by the external voltage in this 1D Rashba ring.

  5. Cooperative Lamb shift in a mesoscopic atomic array.

    PubMed

    Meir, Z; Schwartz, O; Shahmoon, E; Oron, D; Ozeri, R

    2014-11-07

    According to quantum electrodynamics, the exchange of virtual photons in a system of identical quantum emitters causes a shift of its energy levels. Such shifts, known as cooperative Lamb shifts, have been studied mostly in the near-field regime. However, the resonant electromagnetic interaction persists also at large distances, providing coherent coupling between distant atoms. Here, we report a direct spectroscopic observation of the cooperative Lamb shift of an optical electric-dipole transition in an array of Sr(+) ions suspended in a Paul trap at inter-ion separations much larger than the resonance wavelength. By controlling the precise positions of the ions, we studied the far-field resonant coupling in chains of up to eight ions, extending to a length of 40  μm. This method provides a novel tool for experimental exploration of cooperative emission phenomena in extended mesoscopic atomic arrays.

  6. Light fields in complex media: Mesoscopic scattering meets wave control

    NASA Astrophysics Data System (ADS)

    Rotter, Stefan; Gigan, Sylvain

    2017-01-01

    The newly emerging field of wave front shaping in complex media has recently seen enormous progress. The driving force behind these advances has been the experimental accessibility of the information stored in the scattering matrix of a disordered medium, which can nowadays routinely be exploited to focus light as well as to image or to transmit information even across highly turbid scattering samples. An overview of these new techniques, their experimental implementations, and the underlying theoretical concepts following from mesoscopic scattering theory is provided. In particular, the intimate connections between quantum transport phenomena and the scattering of light fields in disordered media, which can both be described by the same theoretical concepts, are highlighted. Particular emphasis is put on how these topics relate to application-oriented research fields such as optical imaging, sensing, and communication.

  7. Mesoscopic Random Lattice Models of Rupture in Rubber

    NASA Astrophysics Data System (ADS)

    Reynolds, David; Marder, Michael

    2006-03-01

    In an earlier work, Marder illustrated how rupture in rubber differs from conventional fracture. Dissipation and toughening of the back edges of ruptures are critical for the propagation of stable ruptures. In this earlier work, mesoscopic models were arrived at by approximating the Mooney-Rivlin theory of rubber by a finite difference scheme on a triangular lattice. From this perspective, qualitatively the lattice sites are considered to be crosslinkers and the bonds are polymers. We extend this work by considering the crosslinkers to be randomly distributed throughout the material rather than being ordered. For both random and ordered lattices, without rupture, there are many different ways to construct free energy functionals that reproduce the continuum theory. However, not all of the constructions are numerically stable. We explore the physical consequences of the disorder and the physical interpretations of the observed numerical instabilities.

  8. Mesoscopic patterns of neural activity support songbird cortical sequences.

    PubMed

    Markowitz, Jeffrey E; Liberti, William A; Guitchounts, Grigori; Velho, Tarciso; Lois, Carlos; Gardner, Timothy J

    2015-06-01

    Time-locked sequences of neural activity can be found throughout the vertebrate forebrain in various species and behavioral contexts. From "time cells" in the hippocampus of rodents to cortical activity controlling movement, temporal sequence generation is integral to many forms of learned behavior. However, the mechanisms underlying sequence generation are not well known. Here, we describe a spatial and temporal organization of the songbird premotor cortical microcircuit that supports sparse sequences of neural activity. Multi-channel electrophysiology and calcium imaging reveal that neural activity in premotor cortex is correlated with a length scale of 100 µm. Within this length scale, basal-ganglia-projecting excitatory neurons, on average, fire at a specific phase of a local 30 Hz network rhythm. These results show that premotor cortical activity is inhomogeneous in time and space, and that a mesoscopic dynamical pattern underlies the generation of the neural sequences controlling song.

  9. Ionization reactions of ion complexes in mesoscopic water clusters

    NASA Astrophysics Data System (ADS)

    Consta, Styliani; Kapral, Raymond

    1999-12-01

    The free energy and dynamics of the dissociation reactions of the [Na+(Cl-)2] ion complex in mesoscopic water clusters are examined. The free energy surface shows the existence of stable single and double solvent-separated complex species formed from ionization of the stable double-contact ion complex. The reaction occurs on the cluster surface for mesoscale clusters composed of tens of water molecules. Passage between stable species is an activated process but barrier crossing has a large diffusive component so that dynamical corrections to transition state theory are large. The structure of the decay of the time-dependent rate constant reflects the diffusive character of the recrossing dynamics so that a plateau is not established on a 10 ps time scale in contrast to ionization dynamics in bulk fluids.

  10. Towards large-scale, human-based, mesoscopic neurotechnologies.

    PubMed

    Chang, Edward F

    2015-04-08

    Direct human brain recordings have transformed the scope of neuroscience in the past decade. Progress has relied upon currently available neurophysiological approaches in the context of patients undergoing neurosurgical procedures for medical treatment. While this setting has provided precious opportunities for scientific research, it also has presented significant constraints on the development of new neurotechnologies. A major challenge now is how to achieve high-resolution spatiotemporal neural recordings at a large scale. By narrowing the gap between current approaches, new directions tailored to the mesoscopic (intermediate) scale of resolution may overcome the barriers towards safe and reliable human-based neurotechnology development, with major implications for advancing both basic research and clinical translation.

  11. Manipulating mesoscopic multipartite entanglement with atom-light interfaces

    SciTech Connect

    Stasinska, J.; Rodo, C.; Paganelli, S.; Birkl, G.; Sanpera, A.

    2009-12-15

    Entanglement between two macroscopic atomic ensembles induced by measurement on an ancillary light system has proven to be a powerful method for engineering quantum memories and quantum state transfer. Here we investigate the feasibility of such methods for generation, manipulation, and detection of genuine multipartite entanglement (Greenberger-Horne-Zeilinger and clusterlike states) between mesoscopic atomic ensembles without the need of individual addressing of the samples. Our results extend in a nontrivial way the Einstein-Podolsky-Rosen entanglement between two macroscopic gas samples reported experimentally in [B. Julsgaard, A. Kozhekin, and E. Polzik, Nature (London) 413, 400 (2001)]. We find that under realistic conditions, a second orthogonal light pulse interacting with the atomic samples, can modify and even reverse the entangling action of the first one leaving the samples in a separable state.

  12. Acoustic dynamics of network-forming glasses at mesoscopic wavelengths

    PubMed Central

    Ferrante, C.; Pontecorvo, E.; Cerullo, G.; Chiasera, A.; Ruocco, G.; Schirmacher, W.; Scopigno, T.

    2013-01-01

    The lack of long-range structural order in amorphous solids induces well known thermodynamic anomalies, which are the manifestation of distinct peculiarities in the vibrational spectrum. Although the impact of such anomalies vanishes in the long wavelength, elastic continuum limit, it dominates at length scales comparable to interatomic distances, implying an intermediate transition regime still poorly understood. Here we report a study of such mesoscopic domains by means of a broadband version of picosecond photo-acoustics, developed to coherently generate and detect hypersonic sound waves in the sub-THz region with unprecedented sampling efficiency. We identify a temperature-dependent fractal v3/2 frequency behaviour of the sound attenuation, pointing to the presence of marginally stable regions and a transition between the two above mentioned limits. The essential features of this behaviour are captured by a theoretical approach based on random spatial variation of the shear modulus, including anharmonic interactions. PMID:23653205

  13. Mesoscopic Patterns of Neural Activity Support Songbird Cortical Sequences

    PubMed Central

    Guitchounts, Grigori; Velho, Tarciso; Lois, Carlos; Gardner, Timothy J.

    2015-01-01

    Time-locked sequences of neural activity can be found throughout the vertebrate forebrain in various species and behavioral contexts. From “time cells” in the hippocampus of rodents to cortical activity controlling movement, temporal sequence generation is integral to many forms of learned behavior. However, the mechanisms underlying sequence generation are not well known. Here, we describe a spatial and temporal organization of the songbird premotor cortical microcircuit that supports sparse sequences of neural activity. Multi-channel electrophysiology and calcium imaging reveal that neural activity in premotor cortex is correlated with a length scale of 100 µm. Within this length scale, basal-ganglia–projecting excitatory neurons, on average, fire at a specific phase of a local 30 Hz network rhythm. These results show that premotor cortical activity is inhomogeneous in time and space, and that a mesoscopic dynamical pattern underlies the generation of the neural sequences controlling song. PMID:26039895

  14. Electron teleportation via Majorana bound states in a mesoscopic superconductor.

    PubMed

    Fu, Liang

    2010-02-05

    Zero-energy Majorana bound states in superconductors have been proposed to be potential building blocks of a topological quantum computer, because quantum information can be encoded nonlocally in the fermion occupation of a pair of spatially separated Majorana bound states. However, despite intensive efforts, nonlocal signatures of Majorana bound states have not been found in charge transport. In this work, we predict a striking nonlocal phase-coherent electron transfer process by virtue of tunneling in and out of a pair of Majorana bound states. This teleportation phenomenon only exists in a mesoscopic superconductor because of an all-important but previously overlooked charging energy. We propose an experimental setup to detect this phenomenon in a superconductor-quantum-spin-Hall-insulator-magnetic-insulator hybrid system.

  15. Mesoscopic mechanical resonators as quantum noninertial reference frames

    NASA Astrophysics Data System (ADS)

    Katz, B. N.; Blencowe, M. P.; Schwab, K. C.

    2015-10-01

    An atom attached to a micrometer-scale wire that is vibrating at a frequency ˜100 MHz and with displacement amplitude ˜1 nm experiences an acceleration magnitude ˜109ms -2 , approaching the surface gravity of a neutron star. As one application of such extreme noninertial forces in a mesoscopic setting, we consider a model two-path atom interferometer with one path consisting of the 100 MHz vibrating wire atom guide. The vibrating wire guide serves as a noninertial reference frame and induces an in principle measurable phase shift in the wave function of an atom traversing the wire frame. We furthermore consider the effect on the two-path atom wave interference when the vibrating wire is modeled as a quantum object, hence functioning as a quantum noninertial reference frame. We outline a possible realization of the vibrating wire, atom interferometer using a superfluid helium quantum interference setup.

  16. Mesoscopic entanglement of atomic ensembles through nonresonant stimulated Raman scattering

    SciTech Connect

    Ji, Wenhai; Wu, Chunbai; Enk, S. J. van; Raymer, M. G.

    2007-05-15

    We propose a scheme of generating and verifying mesoscopic-level entanglement between two atomic ensembles using nonresonant stimulated Raman scattering. Entanglement can be generated by direct detection or balanced homodyne detection of the Stokes fields from the two cells after they interfere on a beam splitter. The entanglement of the collective atomic fields can be transferred to the anti-Stokes fields in a readout process. By measuring the operator moments of the anti-Stokes fields, we can verify the presence of entanglement. We model the effects of practical factors such as Stokes-field detector quantum efficiency and additive thermal noise in the entanglement generating process, and anti-Stokes-field losses in the entanglement verification process, and find achievable regimes in which entanglement can be verified at the levels of tens to hundreds of atomic excitations in the ensembles.

  17. Geometric correlations and breakdown of mesoscopic universality in spin transport.

    PubMed

    Adagideli, I; Jacquod, Ph; Scheid, M; Duckheim, M; Loss, D; Richter, K

    2010-12-10

    We construct a unified semiclassical theory of charge and spin transport in chaotic ballistic and disordered diffusive mesoscopic systems with spin-orbit interaction. Neglecting dynamic effects of spin-orbit interaction, we reproduce the random matrix theory results that the spin conductance fluctuates universally around zero average. Incorporating these effects into the theory, we show that geometric correlations generate finite average spin conductances, but that they do not affect the charge conductance to leading order. The theory, which is confirmed by numerical transport calculations, allows us to investigate the entire range from the weak to the previously unexplored strong spin-orbit regime, where the spin rotation time is shorter than the momentum relaxation time.

  18. On time-dependent counting statistics of mesoscopic electron transport

    NASA Astrophysics Data System (ADS)

    Belzig, Wolfgang

    2009-03-01

    Full counting statistics (FCS) has emerged as a key concept to understand quantum transport in mesoscopic systems like heterostructures, quantum wires, and quantum dots. The knowlegde of the FCS not only enables to predict all measurable zero-frequency quantities accessible via charge detection, but also allows to identify the elementary transport events and the correlations between them. We demonstrate this concept for a standard quantum point contact between normal and/or superconducting leads under dc- and ac-bias. [M. Vanevic, Yu. V. Nazarov, W. Belzig, Phys. Rev. Lett. 99, 076601 (2007)] Finally we address the question, how these concepts can be applied to time-resolved current measurements. [A. Bednorz and W. Belzig, Phys. Rev. Lett. 101, 206803 (2008)

  19. Testing the nematophagous biological control strain Paecilomyces lilacinus 251 for paecilotoxin production.

    PubMed

    Khan, Alamgir; Williams, Keith; Nevalainen, Helena

    2003-10-10

    Paecilomyces lilacinus is a nematophagous fungus currently developed as a biological control agent. In order to evaluate potential toxin production, culture extract and concentrated culture supernatant of P. lilacinus strain 251 were tested against Gram-negative and Gram-positive bacteria. High-performance liquid chromatography analysis was carried out to compare the chromatograms of P. lilacinus strain 251 with the chromatogram of known paecilotoxin. It was found that the 251 strain of P. lilacinus did not produce detectable levels of paecilotoxin or other toxins with antimicrobial activity.

  20. Collaborative testing improves performance but not content retention in a large-enrollment introductory biology class.

    PubMed

    Leight, Hayley; Saunders, Cheston; Calkins, Robin; Withers, Michelle

    2012-01-01

    Collaborative testing has been shown to improve performance but not always content retention. In this study, we investigated whether collaborative testing could improve both performance and content retention in a large, introductory biology course. Students were semirandomly divided into two groups based on their performances on exam 1. Each group contained equal numbers of students scoring in each grade category ("A"-"F") on exam 1. All students completed each of the four exams of the semester as individuals. For exam 2, one group took the exam a second time in small groups immediately following the individually administered test. The other group followed this same format for exam 3. Individual and group exam scores were compared to determine differences in performance. All but exam 1 contained a subset of cumulative questions from the previous exam. Performances on the cumulative questions for exams 3 and 4 were compared for the two groups to determine whether there were significant differences in content retention. Even though group test scores were significantly higher than individual test scores, students who participated in collaborative testing performed no differently on cumulative questions than students who took the previous exam as individuals.

  1. Collaborative Testing Improves Performance but Not Content Retention in a Large-Enrollment Introductory Biology Class

    PubMed Central

    Leight, Hayley; Saunders, Cheston; Calkins, Robin; Withers, Michelle

    2012-01-01

    Collaborative testing has been shown to improve performance but not always content retention. In this study, we investigated whether collaborative testing could improve both performance and content retention in a large, introductory biology course. Students were semirandomly divided into two groups based on their performances on exam 1. Each group contained equal numbers of students scoring in each grade category (“A”–“F”) on exam 1. All students completed each of the four exams of the semester as individuals. For exam 2, one group took the exam a second time in small groups immediately following the individually administered test. The other group followed this same format for exam 3. Individual and group exam scores were compared to determine differences in performance. All but exam 1 contained a subset of cumulative questions from the previous exam. Performances on the cumulative questions for exams 3 and 4 were compared for the two groups to determine whether there were significant differences in content retention. Even though group test scores were significantly higher than individual test scores, students who participated in collaborative testing performed no differently on cumulative questions than students who took the previous exam as individuals. PMID:23222835

  2. Fetal sex chromosome testing by maternal plasma DNA sequencing: clinical laboratory experience and biology.

    PubMed

    Bianchi, Diana W; Parsa, Saba; Bhatt, Sucheta; Halks-Miller, Meredith; Kurtzman, Kathryn; Sehnert, Amy J; Swanson, Amy

    2015-02-01

    To describe the clinical experience with noninvasive prenatal testing for fetal sex chromosomes using sequencing of maternal plasma cell-free DNA in a commercial laboratory. A noninvasive prenatal testing laboratory data set was examined for samples in which fetal sex chromosomes were reported. Available clinical outcomes were reviewed. Of 18,161 samples with sex chromosome results, no sex chromosome aneuploidy was detected in 98.9% and the fetal sex was reported as XY (9,236) or XX (8,721). In 4 of 32 cases in which the fetal sex was reportedly discordant between noninvasive prenatal testing and karyotype or ultrasonogram, a potential biological reason for the discordance exists, including two cases of documented co-twin demise, one case of a maternal kidney transplant from a male donor, and one case of fetal ambiguous genitalia. In the remaining 204 samples (1.1%), one of four sex chromosome aneuploidies (monosomy X, XXX, XXY, or XYY) was detected. The frequency of false positive results for sex chromosome aneuploidies is a minimum of 0.26% and a maximum of 1.05%. All but one of the discordant sex chromosome aneuploidy results involved the X chromosome. In two putative false-positive XXX cases, maternal XXX was confirmed by karyotype. For the false-positive cases, mean maternal age was significantly higher in monosomy X (P<.001) and lower in XXX (P=.008). Noninvasive prenatal testing results for sex chromosome aneuploidy can be confounded by maternal or fetal biological phenomena. When a discordant noninvasive prenatal testing result is encountered, resolution requires additional maternal history, detailed fetal ultrasonography, and determination of fetal and possibly maternal karyotypes.

  3. Chemical analysis and biological testing of materials from the EDS coal liquefaction process: a status report

    SciTech Connect

    Later, D.W.; Pelroy, R.A.; Wilson, B.W.

    1984-05-01

    Representative process materials were obtained from the EDS pilot plant for chemical and biological analyses. These materials were characterized for biological activity and chemical composition using a microbial mutagenicity assay and chromatographic and mass spectrometric analytical techniques. The two highest boiling distillation cuts, as well as process solvent (PS) obtained from the bottoms recycle mode operation, were tested for initiation of mouse skin tumorigenicity. All three materials were active; the crude 800/sup 0 +/F cut was substantially more potent than the crude bottoms recycle PS or 750 to 800/sup 0/F distillate cut. Results from chemical analyses showed the EDS materials, in general, to be more highly alkylated and have higher hydroaromatic content than analogous SRC II process materials (no in-line process hydrogenation) used for comparison. In the microbial mutagenicity assays the N-PAC fractions showed greater activity than did the aliphatic hydrocarbon, hydroxy-PAH, or PAH fractions, although mutagenicity was detected in certain PAH fractions by a modified version of the standard microbial mutagenicity assay. Mutagenic activities for the EDS materials were lower, overall, than those for the corresponding materials from the SRC II process. The EDS materials produced under different operational modes had distinguishable differences in both their chemical constituency and biological activity. The primary differences between the EDS materials studied here and their SRC II counterparts used for comparison are most likely attributable to the incorporation of catalytic hydrogenation in the EDS process. 27 references, 28 figures, 27 tables.

  4. Ac transport properties of electrons in parallel-plate mesoscopic capacitors in series

    NASA Astrophysics Data System (ADS)

    Chuen, J.; Wang, J. H.

    2017-10-01

    In a self-consistent manner by taking into account three aspects: the frequency of the bias, geometry of the capacitor (e.g. plate separation) and the Fermi energy of the system, ac transport properties of electrons in parallel-plate mesoscopic capacitor in series under an bias are discussed. The charge density, the internal characteristic potential caused by electrons interaction and the size-dependent mesoscopic capacitance are calculated. Results show that these quantities are complex number with very small finite imaginary part in mesoscopic scale, and the current conservation is satisfied in our numerical calculation. Moreover, when the plate separation is large enough, the mesoscopic capacitance approaches to the geometric capacitance, and the imaginary parts vanish. When the plate separation is small, there are some differences between them.

  5. Mesoscopic capacitor and zero-point energy: Poisson's distribution for virtual charges, pressure, and decoherence control

    NASA Astrophysics Data System (ADS)

    Flores, J. C.

    2014-08-01

    Mesoscopic capacitor theory, which includes intrinsic inductive effects from quantum tunneling, is applied to conducting spherical shells. The zero-point pressure and the number of virtual charged pairs are determined assuming a Poisson distribution. They are completely defined by a dimensionless mesoscopic parameter (χc) measuring the average number of virtual pairs per solid angle and carrying mesoscopic information. Fluctuations remain finite and well defined. Connections with usual quantum-field-theory limit enables us to evaluate χc 1.007110. Equivalently, for a mesoscopic parallel-plate capacitor, the shot noise distribution becomes operative with χc 0.94705 as well being related to the density of virtual pairs. Temperature decoherence and capacitor control are discussed by considering typical values of quantum dot devices and Coulomb blockade theory.

  6. Electrophoresis tests on STS-3 and ground control experiments - A basis for future biological sample selections

    NASA Technical Reports Server (NTRS)

    Morrison, D. R.; Lewis, M. L.

    1982-01-01

    Static zone electrophoresis is an electrokinetic method of separating macromolecules and small particles. However, its application for the isolation of biological cells and concentrated protein solutions is limited by sedimentation and convection. Microgravity eliminates or reduces sedimentation, floatation, and density-driven convection arising from either Joule heating or concentration differences. The advantages of such an environment were first demonstrated in space during the Apollo 14 and 16 missions. In 1975 the Electrophoresis Technology Experiment (MA-011) was conducted during the Apollo-Soyuz Test Project flight. In 1979 a project was initiated to repeat the separations of human kidney cells. One of the major objectives of the Electrophoresis Equipment Verification Tests (EEVT) on STS-3 was to repeat and thereby validate the first successful electrophoretic separation of human kidney cells. Attention is given to the EEVT apparatus, the preflight electrophoresis, and inflight operational results.

  7. Molecular and biological diagnostic tests for monitoring benzimidazole resistance in human soil-transmitted helminths.

    PubMed

    Diawara, Aïssatou; Schwenkenbecher, Jan M; Kaplan, Ray M; Prichard, Roger K

    2013-06-01

    In endemic countries with soil-transmitted helminths mass drug administration with albendazole or mebendazole are being implemented as a control strategy. However, it is well known in veterinary helminths that the use of the same benzimidazole drugs can place selection on the β-tubulin gene, leading to resistance. Given the concern that resistance could arise in human soil-transmitted helminths, there is an urgent need to develop accurate diagnostic tools for monitoring resistance. In this study, we developed molecular assays to detect putative resistance genetic changes in Ascaris lumbricoides, Trichuris trichiura, and hookworms, and we optimized an egg hatch assay for the canine hookworm Ancylostoma caninum and applied it to Necator americanus. Both assays were tested on field samples. The molecular assays demonstrated their reproducibility and capacity to detect the presence of worms carrying putative resistance-associated genetic changes. However, further investigations are needed to validate our molecular and biological tests on additional field isolates.

  8. Design, Fabrication and Characterization of a Pure Uniaxial Microloading System for Biologic Testing

    PubMed Central

    King, Jonathan D.; York, Spencer L.; Saunders, Marnie M.

    2016-01-01

    The field of mechanobiology is aimed at understanding the role the mechanical environment plays in directing cell and tissue development, function and disease. The empirical aspect of the field requires the development of accurate, reproducible and reliable loading platforms that can apply microprecision mechanical load. In this study we designed, fabricated and characterized a pure uniaxial loading platform capable of testing small synthetic and organic specimens along a horizontal axis. The major motivation for platform development was in stimulating bone cells seeded on elastomeric substrates and soft tissue loading. The biological uses required the development of culturing fixtures and environmental chamber. The device utilizes commercial microactuators, load cells and a rail/carriage block system. Following fabrication, acceptable performance was verified by suture tensile testing. PMID:26904918

  9. Comparison between Lagrangian and mesoscopic Eulerian modelling approaches for inertial particles suspended in decaying isotropic turbulence

    NASA Astrophysics Data System (ADS)

    Kaufmann, A.; Moreau, M.; Simonin, O.; Helie, J.

    2008-06-01

    The purpose of this paper is to evaluate the accuracy of the mesoscopic approach proposed by Février et al. [P. Février, O. Simonin, K.D. Squires, Partitioning of particle velocities in gas-solid turbulent flows into a continuous field and a spatially uncorrelated random distribution: theoretical formalism and numerical study, J. Fluid Mech. 533 (2005) 1-46] by comparison against the Lagrangian approach for the simulation of an ensemble of non-colliding particles suspended in a decaying homogeneous isotropic turbulence given by DNS. The mesoscopic Eulerian approach involves to solve equations for a few particle PDF moments: number density, mesoscopic velocity, and random uncorrelated kinetic energy (RUE), derived from particle flow ensemble averaging conditioned by the turbulent fluid flow realization. In addition, viscosity and diffusivity closure assumptions are used to compute the unknown higher order moments which represent the mesoscopic velocity and RUE transport by the uncorrelated velocity component. A detailed comparison between the two approaches is carried out for two different values of the Stokes number based on the initial fluid Kolmogorov time scale, St=0.17 and 2.2. In order to perform reliable comparisons for the RUE local instantaneous distribution and for the mesoscopic kinetic energy spectrum, the error due to the computation method of mesoscopic quantities from Lagrangian simulation results is evaluated and minimized. A very good agreement is found between the mesoscopic Eulerian and Lagrangian predictions for the small particle Stokes number case corresponding to the smallest particle inertia. For larger particle inertia, a bulk viscous term is included in the mesoscopic velocity governing equation to avoid spurious spatial oscillation that may arise due to the inability of the numerical scheme to resolve sharp number density gradients. As a consequence, for St=2.2, particle number density and RUE spatial distribution predicted by the

  10. Covariance Association Test (CVAT) Identifies Genetic Markers Associated with Schizophrenia in Functionally Associated Biological Processes.

    PubMed

    Rohde, Palle Duun; Demontis, Ditte; Cuyabano, Beatriz Castro Dias; Børglum, Anders D; Sørensen, Peter

    2016-08-01

    Schizophrenia is a psychiatric disorder with large personal and social costs, and understanding the genetic etiology is important. Such knowledge can be obtained by testing the association between a disease phenotype and individual genetic markers; however, such single-marker methods have limited power to detect genetic markers with small effects. Instead, aggregating genetic markers based on biological information might increase the power to identify sets of genetic markers of etiological significance. Several set test methods have been proposed: Here we propose a new set test derived from genomic best linear unbiased prediction (GBLUP), the covariance association test (CVAT). We compared the performance of CVAT to other commonly used set tests. The comparison was conducted using a simulated study population having the same genetic parameters as for schizophrenia. We found that CVAT was among the top performers. When extending CVAT to utilize a mixture of SNP effects, we found an increase in power to detect the causal sets. Applying the methods to a Danish schizophrenia case-control data set, we found genomic evidence for association of schizophrenia with vitamin A metabolism and immunological responses, which previously have been implicated with schizophrenia based on experimental and observational studies. Copyright © 2016 by the Genetics Society of America.

  11. Mesoscopic model and free energy landscape for protein-DNA binding sites: analysis of cyanobacterial promoters.

    PubMed

    Tapia-Rojo, Rafael; Mazo, Juan José; Hernández, José Ángel; Peleato, María Luisa; Fillat, María F; Falo, Fernando

    2014-10-01

    The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes. We use a computational method to analyze promoters from a given genome. Our approach is based on a physical model at the mesoscopic level of protein-DNA interaction based on the influence of DNA local conformation on the dynamics of a general particle along the chain. Following the proposed model, the joined dynamics of the protein particle and the DNA portion of interest, only characterized by its base pair sequence, is simulated. The simulation output is analyzed by generating and analyzing the Free Energy Landscape of the system. In order to prove the capacity of prediction of our computational method we have analyzed nine promoters of Anabaena PCC 7120. We are able to identify the transcription starting site of each of the promoters as the most populated macrostate in the dynamics. The developed procedure allows also to characterize promoter macrostates in terms of thermo-statistical magnitudes (free energy and entropy), with valuable biological implications. Our results agree with independent previous experimental results. Thus, our methods appear as a powerful complementary tool for identifying protein binding sites in promoter sequences.

  12. Pre-release efficacy test of the prospective biological control agent Arytinnis hakani on the invasive weed Genista monspessulana

    USDA-ARS?s Scientific Manuscript database

    In weed biological control, conducting a pre-release efficacy test can help ascertain if prospective biological control agents will be capable of controlling the target plant. Currently, the phloem-feeding psyllid, Arytinnis hakani, is being evaluated as a prospective agent for the exotic invasive w...

  13. A new approach to mechanical testing and modeling of biological tissues, with application to blood vessels.

    PubMed

    Brossollet, L J; Vito, R P

    1996-11-01

    The collection and processing of data from mechanical tests of biological tissues usually follow classical principles appropriate for studying engineering materials. However, difficulties specific to biological tissues have generally kept such methods from producing quantitative results for statistically-oriented studies. This paper demonstrates a different approach linking testing and data reduction with modern statistical tools. Experimental design theory is used to minimize the detrimental effects of collinearity on the stability of the parameters in constitutive equations. The numerical effects of time-dependent biasing factors such as viscoelasticity are reduced by randomizing the order of collection of data points. Some of the parameters of the model are allowed to vary from specimen to specimen while the others are computed once from a database of designed experiments on several specimens. Finally, a new self-modeling algorithm based on principal component analysis is used to generate uncorrelated parameters for a model that is linear in its specimen-dependent parameters. The method, associated with a recently published complementary energy formulation for vascular mechanics, is illustrated with biaxial canine saphenous vein data. Results show that three specimen-dependent linear parameters are enough to characterize the experimental data and that they can be repeatedly estimated from different data sets. Independently collected biaxial inflation data can also be predicted reasonably well with this model.

  14. In silico model-based inference: a contemporary approach for hypothesis testing in network biology

    PubMed Central

    Klinke, David J.

    2014-01-01

    Inductive inference plays a central role in the study of biological systems where one aims to increase their understanding of the system by reasoning backwards from uncertain observations to identify causal relationships among components of the system. These causal relationships are postulated from prior knowledge as a hypothesis or simply a model. Experiments are designed to test the model. Inferential statistics are used to establish a level of confidence in how well our postulated model explains the acquired data. This iterative process, commonly referred to as the scientific method, either improves our confidence in a model or suggests that we revisit our prior knowledge to develop a new model. Advances in technology impact how we use prior knowledge and data to formulate models of biological networks and how we observe cellular behavior. However, the approach for model-based inference has remained largely unchanged since Fisher, Neyman and Pearson developed the ideas in the early 1900’s that gave rise to what is now known as classical statistical hypothesis (model) testing. Here, I will summarize conventional methods for model-based inference and suggest a contemporary approach to aid in our quest to discover how cells dynamically interpret and transmit information for therapeutic aims that integrates ideas drawn from high performance computing, Bayesian statistics, and chemical kinetics. PMID:25139179

  15. Gene expression-based biological test for major depressive disorder: an advanced study

    PubMed Central

    Watanabe, Shin-ya; Numata, Shusuke; Iga, Jun-ichi; Kinoshita, Makoto; Umehara, Hidehiro; Ishii, Kazuo; Ohmori, Tetsuro

    2017-01-01

    Purpose Recently, we could distinguished patients with major depressive disorder (MDD) from nonpsychiatric controls with high accuracy using a panel of five gene expression markers (ARHGAP24, HDAC5, PDGFC, PRNP, and SLC6A4) in leukocyte. In the present study, we examined whether this biological test is able to discriminate patients with MDD from those without MDD, including those with schizophrenia and bipolar disorder. Patients and methods We measured messenger ribonucleic acid expression levels of the aforementioned five genes in peripheral leukocytes in 17 patients with schizophrenia and 36 patients with bipolar disorder using quantitative real-time polymerase chain reaction (PCR), and we combined these expression data with our previous expression data of 25 patients with MDD and 25 controls. Subsequently, a linear discriminant function was developed for use in discriminating between patients with MDD and without MDD. Results This expression panel was able to segregate patients with MDD from those without MDD with a sensitivity and specificity of 64% and 67.9%, respectively. Conclusion Further research to identify MDD-specific markers is needed to improve the performance of this biological test. PMID:28260899

  16. In silico model-based inference: a contemporary approach for hypothesis testing in network biology.

    PubMed

    Klinke, David J

    2014-01-01

    Inductive inference plays a central role in the study of biological systems where one aims to increase their understanding of the system by reasoning backwards from uncertain observations to identify causal relationships among components of the system. These causal relationships are postulated from prior knowledge as a hypothesis or simply a model. Experiments are designed to test the model. Inferential statistics are used to establish a level of confidence in how well our postulated model explains the acquired data. This iterative process, commonly referred to as the scientific method, either improves our confidence in a model or suggests that we revisit our prior knowledge to develop a new model. Advances in technology impact how we use prior knowledge and data to formulate models of biological networks and how we observe cellular behavior. However, the approach for model-based inference has remained largely unchanged since Fisher, Neyman and Pearson developed the ideas in the early 1900s that gave rise to what is now known as classical statistical hypothesis (model) testing. Here, I will summarize conventional methods for model-based inference and suggest a contemporary approach to aid in our quest to discover how cells dynamically interpret and transmit information for therapeutic aims that integrates ideas drawn from high performance computing, Bayesian statistics, and chemical kinetics.

  17. High Resolution Higher Energy X-ray Microscope for Mesoscopic Materials

    NASA Astrophysics Data System (ADS)

    Snigireva, I.; Snigirev, A.

    2013-10-01

    We developed a novel X-ray microscopy technique to study mesoscopically structured materials, employing compound refractive lenses. The easily seen advantage of lens-based methodology is the possibility to retrieve high resolution diffraction pattern and real-space images in the same experimental setup. Methodologically the proposed approach is similar to the studies of crystals by high resolution transmission electron microscopy. The proposed microscope was applied for studying of mesoscopic materials such as natural and synthetic opals, inverted photonic crystals.

  18. Chaste: A test-driven approach to software development for biological modelling

    NASA Astrophysics Data System (ADS)

    Pitt-Francis, Joe; Pathmanathan, Pras; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Fletcher, Alexander G.; Mirams, Gary R.; Murray, Philip; Osborne, James M.; Walter, Alex; Chapman, S. Jon; Garny, Alan; van Leeuwen, Ingeborg M. M.; Maini, Philip K.; Rodríguez, Blanca; Waters, Sarah L.; Whiteley, Jonathan P.; Byrne, Helen M.; Gavaghan, David J.

    2009-12-01

    Chaste ('Cancer, heart and soft-tissue environment') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence. Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling. Program summaryProgram title: Chaste Catalogue identifier: AEFD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: LGPL 2.1 No. of lines in distributed program, including test data, etc.: 5 407 321 No. of bytes in distributed program, including test data, etc.: 42 004 554 Distribution format: tar.gz Programming language: C++ Operating system: Unix Has the code been vectorised or parallelized?: Yes. Parallelized using MPI. RAM:<90 Megabytes for two of the scenarios described in Section 6 of the manuscript (Monodomain re-entry on a slab or Cylindrical crypt simulation). Up to 16 Gigabytes (distributed across processors) for full resolution bidomain cardiac simulation. Classification: 3. External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, Xerces Nature of problem: Chaste may be used for solving coupled ODE and PDE systems arising from modelling biological systems. Use of Chaste in two application areas are described in this paper: cardiac electrophysiology and

  19. Revocation of General Safety Test Regulations That Are Duplicative of Requirements in Biologics License Applications. Final rule.

    PubMed

    2015-07-02

    The Food and Drug Administration (FDA) is amending the biologics regulations by removing the general safety test (GST) requirements for biological products. FDA is finalizing this action because the existing codified GST regulations are duplicative of requirements that are also specified in biologics license applications (BLAs), or are no longer necessary or appropriate to help ensure the safety, purity, and potency of licensed biological products. FDA is taking this action as part of its retrospective review of its regulations to promote improvement and innovation, in response to the Executive order.

  20. [Prediction of Post-operative Lymph Node Metastasis with a Molecular Biological Test in Head and Neck Cancer].

    PubMed

    Takahashi, Katsumasa; Nakajima, Kyoko; Shino, Masato; Toyoda, Minoru; Takayasu, Yukihiro; Chikamatsu, Kazuaki

    2015-02-01

    We assessed herein the post-operative lymph node metastasis in head and neck cancer, using the One-step nucleotide amplification (OSNA) method targeting matrix metalloproteinase 7 (MMP-7). Compared with the pathological test, the molecular biological test revealed more lymph node metastasis, resulting in poor prognosis. Six cases, of which the number of lymph node metastasis was the same between pathological and molecular biological test, survived. On the other hand, three of four cases, in which number of lymph node metastasis in the molecular biological test were larger than the pathological test, died from metastasis. We concluded that the pathological test underestimated metastasis, and OSNA with MMP-7 was useful for the prediction of post-operative lymph node metastasis.

  1. Using polyclonal and monoclonal antibodies in regulatory testing of biological products.

    PubMed

    Coe Clough, Nancy E; Hauer, Paul J

    2005-01-01

    Polyclonal and monoclonal antibodies are often used in regulatory testing of biologicals (vaccines and related products). One of the most common applications for antibody-based immunoassays is as a batch release test. Batch release tests, whether they measure serological responses to vaccination or they quantify individual antigens by in vitro methods, must provide an acceptable estimate of potency of an individual batch of vaccine. Thus, due consideration must be given to the type of antibody used or quantified in such assays. Differences in specificity and avidity may affect the utility of an assay as an indicator of potency; case examples are given to illustrate these concepts. Concerns associated with antigen quantification assays (e.g., reagent denaturation upon binding to solid substrates, and interference from nontarget antigens or additives in a complex vaccine) are also discussed. International efforts to harmonize test methods in recent years have increased the importance of establishing standardized antibodies. Sources of such antibodies and issues associated with the ongoing availability of antibody supplies are described.

  2. Biology-inspired Microphysiological System Approaches to Solve the Prediction Dilemma of Substance Testing

    PubMed Central

    Marx, Uwe; Andersson, Tommy B.; Bahinski, Anthony; Beilmann, Mario; Beken, Sonja; Cassee, Flemming R.; Cirit, Murat; Daneshian, Mardas; Fitzpatrick, Susan; Frey, Olivier; Gaertner, Claudia; Giese, Christoph; Griffith, Linda; Hartung, Thomas; Heringa, Minne B.; Hoeng, Julia; de Jong, Wim H.; Kojima, Hajime; Kuehnl, Jochen; Luch, Andreas; Maschmeyer, Ilka; Sakharov, Dmitry; Sips, Adrienne J. A. M.; Steger-Hartmann, Thomas; Tagle, Danilo A.; Tonevitsky, Alexander; Tralau, Tewes; Tsyb, Sergej; van de Stolpe, Anja; Vandebriel, Rob; Vulto, Paul; Wang, Jufeng; Wiest, Joachim; Rodenburg, Marleen; Roth, Adrian

    2017-01-01

    Summary The recent advent of microphysiological systems – microfluidic biomimetic devices that aspire to emulate the biology of human tissues, organs and circulation in vitro – is envisaged to enable a global paradigm shift in drug development. An extraordinary US governmental initiative and various dedicated research programs in Europe and Asia have led recently to the first cutting-edge achievements of human single-organ and multi-organ engineering based on microphysiological systems. The expectation is that test systems established on this basis would model various disease stages, and predict toxicity, immunogenicity, ADME profiles and treatment efficacy prior to clinical testing. Consequently, this technology could significantly affect the way drug substances are developed in the future. Furthermore, microphysiological system-based assays may revolutionize our current global programs of prioritization of hazard characterization for any new substances to be used, for example, in agriculture, food, ecosystems or cosmetics, thus, replacing laboratory animal models used currently. Thirty-five experts from academia, industry and regulatory bodies present here the results of an intensive workshop (held in June 2015, Berlin, Germany). They review the status quo of microphysiological systems available today against industry needs, and assess the broad variety of approaches with fit-for-purpose potential in the drug development cycle. Feasible technical solutions to reach the next levels of human biology in vitro are proposed. Furthermore, key organ-on-a-chip case studies, as well as various national and international programs are highlighted. Finally, a roadmap into the future is outlined, to allow for more predictive and regulatory-accepted substance testing on a global scale. PMID:27180100

  3. Biology-inspired microphysiological system approaches to solve the prediction dilemma of substance testing.

    PubMed

    Marx, Uwe; Andersson, Tommy B; Bahinski, Anthony; Beilmann, Mario; Beken, Sonja; Cassee, Flemming R; Cirit, Murat; Daneshian, Mardas; Fitzpatrick, Susan; Frey, Olivier; Gaertner, Claudia; Giese, Christoph; Griffith, Linda; Hartung, Thomas; Heringa, Minne B; Hoeng, Julia; de Jong, Wim H; Kojima, Hajime; Kuehnl, Jochen; Leist, Marcel; Luch, Andreas; Maschmeyer, Ilka; Sakharov, Dmitry; Sips, Adrienne J A M; Steger-Hartmann, Thomas; Tagle, Danilo A; Tonevitsky, Alexander; Tralau, Tewes; Tsyb, Sergej; van de Stolpe, Anja; Vandebriel, Rob; Vulto, Paul; Wang, Jufeng; Wiest, Joachim; Rodenburg, Marleen; Roth, Adrian

    2016-01-01

    The recent advent of microphysiological systems - microfluidic biomimetic devices that aspire to emulate the biology of human tissues, organs and circulation in vitro - is envisaged to enable a global paradigm shift in drug development. An extraordinary US governmental initiative and various dedicated research programs in Europe and Asia have led recently to the first cutting-edge achievements of human single-organ and multi-organ engineering based on microphysiological systems. The expectation is that test systems established on this basis would model various disease stages, and predict toxicity, immunogenicity, ADME profiles and treatment efficacy prior to clinical testing. Consequently, this technology could significantly affect the way drug substances are developed in the future. Furthermore, microphysiological system-based assays may revolutionize our current global programs of prioritization of hazard characterization for any new substances to be used, for example, in agriculture, food, ecosystems or cosmetics, thus, replacing laboratory animal models used currently. Thirty-six experts from academia, industry and regulatory bodies present here the results of an intensive workshop (held in June 2015, Berlin, Germany). They review the status quo of microphysiological systems available today against industry needs, and assess the broad variety of approaches with fit-for-purpose potential in the drug development cycle. Feasible technical solutions to reach the next levels of human biology in vitro are proposed. Furthermore, key organ-on-a-chip case studies, as well as various national and international programs are highlighted. Finally, a roadmap into the future is outlined, to allow for more predictive and regulatory-accepted substance testing on a global scale.

  4. The Closed Equilibrated Biological Aquatic System: A 12 months Test of an Artificial Aquatic Ecosystem

    NASA Astrophysics Data System (ADS)

    Blüm, V.; Andriske, M.; Ludwig, Ch.; Paaßen, U.; Voeste, D.

    1999-01-01

    The ``Closed Equilibrated Biological Aquatic System'' (C.E.B.A.S.) is finally disposed for long-term multi-generation experiments with aquatic organisms in a space station. Therefore a minimum operation time of three month is required. It is verified in three versions of laboratory prototypes. The third one passed successfully a 12 months mid-term test in 1995/96 thus demonstrating its high biological stability. The third version of the C.E.B.A.S. consists of a 100 l animal tank, two plant cultivators with a volume of 15 l each with independent illuminations, a 3.0 l semibiological ``mechanical'' filter, a 3.0 l bacteria filter, a heating/cooling device and a dummy filter unit. The live-bearing teleost Xiphophorus helleri is the vertebrate and the pulmonate water snail Biomphalaria glabrata the invertebrate experimental animal in the system. The rootless higher water plant Ceratophyllum demersum is the producer organism. Ammonia oxidizing bacteria and other microorganisms settle in the filters. A simple data acquisition is combined with temperature and plant illumination control. Besides of the space aspects the C.E.B.A.S. proved to be an extremely suitable tool to investigate the organism and subcomponent interactions in a well defined terrestrial aquatic closed ecosystem by providing physical, chemical and biological data which allow an approach to a comprehensive system analysis. Moreover the C.E.B.A.S. is the base for the development of innovative combined animal-plant aquaculture systems for human nutrition on earth which could be implemented into bioregenerative life support systems with a higher degree of complexity suitable for lunar or planetary bases.

  5. The closed equilibrated biological aquatic system: a 12 months test of an artificial aquatic ecosystem.

    PubMed

    Blum, V; Andriske, M; Ludwig, C h; Paassen, U; Voeste, D

    1999-01-01

    The Closed Equilibrated Biological Aquatic System" (C.E.B.A.S.) is finally disposed for long-term multi-generation experiments with aquatic organisms in a space station. Therefore a minimum operation time of three months is required. It is verified in three versions of laboratory prototypes. The third one passed successfully a 12 months mid-term test in 1995/96 thus demonstrating its high biological stability. The third version of the C.E.B.A.S. consists of a 100 l animal tank, two plant cultivators with a volume of 15 l each with independent illuminations, a 3.0 l semibiological "mechanical" filter, a 3.0 l bacteria filter, a heating/cooling device and a dummy filter unit. The live-bearing teleost Xiphophorus helleri is the vertebrate and the pulmonate water snail Biomphalana glabrata the invertebrate experimental animal in the system. The rootless higher water plant Ceratophyllum demersum is the producer organism. Ammonia oxidizing bacteria and other microorganisms settle in the filters. A sample data acquisition is combined with temperature and plant illumination control. Besides of the space aspects the C.E.B.A.S. proved to be an extremely suitable tool to investigate the organism and subcomponent interactions in a well defined terrestrial aquatic closed ecosystem by providing physical, chemical and biological data which allow an approach to a comprehensive system analysis. Moreover the C.E.B.A.S. is the base for the development of innovative combined animal-plant aquaculture systems for human nutrition on earth which could be implemented into bioregenerative life support systems with a higher degree of complexity suitable for lunar or planetary bases.

  6. Magnetic response measurements of mesoscopic superconducting and normal metal rings

    NASA Astrophysics Data System (ADS)

    Bluhm, Hendrik

    The main part of this thesis reports three experiments on the magnetic response of mesoscopic superconducting and normal metal rings using a scanning SQUID microscope. The first experiment explores the magnetic response and fluxoid transitions of superconducting, mesoscopic bilayer aluminum rings in the presence of two coupled order parameters arising from the layered structure. For intermediate couplings, metastable states that have different phase winding numbers around the ring in each of the two order parameters were observed. Larger coupling locks the relative phase, so that the two order parameters are only manifest in the temperature dependence of the response. With increasing proximitization, this signature gradually disappears. The data can be described with a two-order-parameter Ginzburg-Landau theory. The second experiment concentrates on fluxoid transitions in similar, but single-layer rings. Near the critical temperature, the transitions, which are induced by applying a flux to the ring, only admit a single fluxoid at a time. At lower temperatures, several fluxoids enter or leave at once, and the final state approaches the ground state. Currently available theoretical frameworks cannot quantitatively explain the data. Heating and quasiparticle diffusion are likely important for a quantitative understanding of this experiment, which could provide a model system for studying the nonlinear dynamics of superconductors far from equilibrium. The third and most important scanning SQUID study concerns 33 individual mesoscopic gold rings. All measured rings show a paramagnetic linear susceptibility and a poorly understood anomaly around zero field, both of which are likely due to unpaired defect spins. The response of sufficiently small rings also has a component that is periodic in the flux through the ring, with a period close to h/e. Its amplitude varies in sign and magnitude from ring to ring, and its typical value and temperature dependence agree with

  7. A test of biological trait analysis with nematodes and an anthropogenic stressor.

    PubMed

    Mitwally, Hanan M; Fleeger, John W

    2016-03-01

    Aquatic ecosystems are fundamentally altered by nutrient enrichment, and effective monitoring tools are needed to detect biological responses especially in the early stages of eutrophication. We tested the utility of biological trait analysis (BTA) to quantify the temporal responses of nematodes inhabiting salt marsh creeks that were experimentally enriched with nutrients for 6 years. Feeding, body shape, and tail shape traits were characterized on >6000 nematodes from annual samples from enriched and non-enriched sites. Here, we ask if trait combinations are more effective than single traits in detecting the magnitude and rate of change. We also sought to identify combinations of traits that best distinguish natural from nutrient-induced variation. BTA revealed that feeding, body shape, and all traits combined equally detected the response to nutrient enrichment. Compared to single traits however, BTAs were more sensitive to temporal trends and better distinguished natural variation from the response to nutrient enrichment. Tail shape traits (that might respond to altered sediment texture or geochemistry) were not affected by enrichment, and feeding traits yielded the greatest difference between enriched and reference communities indicating that changes in food resources drove responses. Feeding traits provided the highest quality information content in our study, and the use of feeding traits alone may adequately identify anthropogenic effects in many studies. However, we caution that body shape, tail shape, and feeding traits were strongly interrelated at our study site, and a diversity of trait groups may increase the information content of BTAs in more diverse habitats.

  8. Porcine ear skin as a biological substrate for in vitro testing of sunscreen performance.

    PubMed

    Sohn, Myriam; Korn, Verena; Imanidis, Georgios

    2015-01-01

    The purpose of the study was to examine the use of skin from porcine ears as a biological substrate for in vitro testing of sunscreens in order to overcome the shortcomings of the presently used polymethylmethacrylate (PMMA) plates that generally fail to yield a satisfactory correlation between sun protection factors (SPF) in vitro and in vivo. Trypsin-separated stratum corneum and heat-separated epidermis provided UV-transparent substrates that were laid on quartz or on PMMA plates. These were used to determine surface roughness by chromatic confocal imaging and to measure SPF in vitro of 2 sunscreens by diffuse transmission spectroscopy. The recovered skin layers showed a lower roughness than full-thickness skin but yielded SPF in vitro values that more accurately reflected the SPF determined in vivo by a validated procedure than PMMA plates, although the latter had in part roughness values identical to those of intact skin. Combination of skin tissue with a high roughness PMMA plate also provided accurate SPF in vitro. Besides roughness, the improved affinity of the sunscreen to the skin substrate compared to PMMA plates may explain the better in vitro prediction of SPF achieved with the use of a biological substrate. © 2014 S. Karger AG, Basel.

  9. Low-dimensional electron transport in mesoscopic semiconductor devices

    NASA Astrophysics Data System (ADS)

    Martin, Theodore Peyton

    Recent advances in solid state materials engineering have led to mesoscopic devices with feature sizes that approach the fundamental quantum wavelength of charge carriers in the solid, allowing for the experimental observation of quantum interference. By confining carriers to a single quantum state in one or more dimensions, the degrees of freedom for charge transport can be reduced to achieve new device functionality. This dissertation focuses on mesoscopic electron billiards that combine the aspects of zero, one, and two-dimensional transport into one system. Low-temperature measurement of billiards fabricated within a relatively defect-free semiconductor heterostructure results in ballistic transport, where the electron waves follow classical trajectories and the confining walls play a major role in determining the electron interference. Billiards have been traditionally formed by applying a bias to patterned surface gates atop an AlGaAs/GaAs heterostructure. Within this system, fractal fluctuations in the billiard conductance are observed as a function of an applied external magnetic field. These fluctuations are tied to quantum interference via an empirical parameter that describes the resolution of energy levels within the billiard. To investigate whether fractal fluctuations are a robust phenomenon intrinsic to billiard-like structures, this study centers on billiards defined by etching walls into a GaInAs/InP heterostructure, departing from the traditional system in both the type of confinement and material system used. It is expected that etched walls will provide a steeper confinement profile leading to well-defined device shapes. Conductance measurements through the one-dimensional leads that couple electrons into the billiard are utilized in combination with a self-consistent Schrodinger/Poisson solution to demonstrate a steeper confinement potential. Experiments are also carried out to determine whether fractal fluctuations persist when billiards are

  10. Mesoscopic correlation within transmitted speckle pattern and wave localization

    NASA Astrophysics Data System (ADS)

    Hu, Bing

    This thesis is an experimental study of the statistical character of the field distribution within one-dimensional and transmitted through quasi-1D random samples. We measured the spatial extent of the field for extended, evanescent, and localized wave in random single-mode waveguide. We find that spectrally and spatially overlapping modes in a nominally localized region of an open dissipative system can be decomposed into quasi-normal-modes. Microwave field measurements of the near-field transmitted speckle pattern through random quasi-one-dimensional samples were carried out with polarization rotation, along a line, on a tight grid covering the full output surface. The field spectrum is Fourier transformed to give the temporal evolution of the speckle pattern. Field and intensity correlation versus displacement, frequency shift, and polarization rotation were studied to exhibit the growing impact of mesoscopic fluctuation and photon localization with time delay from a exciting pulse. The variation of key distributions and correlation functions with delay time were examined. We find a universal expression for the intensity correlation function which is valid for localized and diffusive waves in steady-state and in the time domain. It is a function only of the field correlation function which is the same in steady state and in the time domain and the degree of correlation, kappa, which also indicates the closeness of the random system to the localization transition. We also studied the microstatistics of the transmitted field in individual sample realizations, as opposed to the traditional focus on fluctuations relative to the ensemble average. We find that the field distribution in each configuration is Gaussian and that mesoscopic correlation arises as a result of fluctuation of the total transmission. The degree of correlation kappa is just the variance of total transmission normalized by its ensemble average. Other aspects on phase statistics of the speckle

  11. The use of crab-shell chitin for biological denitrification: batch and column tests.

    PubMed

    Robinson-Lora, Mary Ann; Brennan, Rachel A

    2009-01-01

    Crab-shell chitin (SC-20) was evaluated for its ability to enhance biological denitrification in bench-scale tests. In the presence of SC-20, highly reducing conditions were generated, supporting both denitrification and sulfate reduction of aerated water. Rapid degradation of protein in SC-20 was observed to cause an initial high release of ammonium and carbon, while a slower, continuous release of calcium carbonate from the crab shell maintained the pH near 9 throughout the tests. In batch tests, denitrification rates of 2.4+/-0.2 mg N/L-d were obtained. Columns receiving a continuous nitrate load of 24.5 mg N/L-d sustained complete denitrification for an average of 149 d (250 pore volumes). The denitrification rates and longevity of SC-20 chitin are comparable to, or better than, those previously reported for other polymeric substrates. This, in addition to its particle size, non-swelling nature, and ease of delivery in slurry form make SC-20 an attractive electron donor source for groundwater bio-denitrification.

  12. [The investigation of nickel dissolution from nitinol under different extraction conditions in biological tests].

    PubMed

    Wen, Xiantao; He, Xueying; Li, Jian; Tang, Juli; Huang, Yongfu

    2013-03-01

    The dissolution of nickel from nitinol alloy under different extraction conditions was investigated when biological tests of nitinol medical devices were carried out. It discussed the equivalence of these extraction conditions and found the best extraction conditions. In the experiment, two brands of nitinol were chosen and extracted under different extraction conditions according to GB/T 16886-12. Plasma emission spectrometer was used to analyse the concentration of nickel in extract liquid. The results show that there is no equivalence among these extraction conditions for nitinol materials. And it is suggested that (37 +/- 1) degree C, (72 +/- 2) h could be used as normal extraction condition and (70 +/- 2) degrees C, (24 +/- 2) h as accelerated extraction condition.

  13. Novel Biological Approaches for Testing the Contributions of Single DSBs and DSB Clusters to the Biological Effects of High LET Radiation.

    PubMed

    Mladenova, Veronika; Mladenov, Emil; Iliakis, George

    2016-01-01

    The adverse biological effects of ionizing radiation (IR) are commonly attributed to the generation of DNA double-strand breaks (DSBs). IR-induced DSBs are generated by clusters of ionizations, bear damaged terminal nucleotides, and frequently comprise base damages and single-strand breaks in the vicinity generating a unique DNA damage-clustering effect that increases DSB "complexity." The number of ionizations in clusters of different radiation modalities increases with increasing linear energy transfer (LET), and is thought to determine the long-known LET-dependence of the relative biological effectiveness (RBE). Multiple ionizations may also lead to the formation of DSB clusters, comprising two or more DSBs that destabilize chromatin further and compromise overall processing. DSB complexity and DSB-cluster formation are increasingly considered in the development of mathematical models of radiation action, which are then "tested" by fitting available experimental data. Despite a plethora of such mathematical models the ultimate goal, i.e., the "a priori" prediction of the radiation effect, has not yet been achieved. The difficulty partly arises from unsurmountable difficulties in testing the fundamental assumptions of such mathematical models in defined biological model systems capable of providing conclusive answers. Recently, revolutionary advances in methods allowing the generation of enzymatic DSBs at random or in well-defined locations in the genome, generate unique testing opportunities for several key assumptions frequently fed into mathematical modeling - including the role of DSB clusters in the overall effect. Here, we review the problematic of DSB-cluster formation in radiation action and present novel biological technologies that promise to revolutionize the way we address the biological consequences of such lesions. We describe new ways of exploiting the I-SceI endonuclease to generate DSB-clusters at random locations in the genome and describe the

  14. Mesoscopic structure of neuronal tracts from time-dependent diffusion.

    PubMed

    Burcaw, Lauren M; Fieremans, Els; Novikov, Dmitry S

    2015-07-01

    Interpreting brain diffusion MRI measurements in terms of neuronal structure at a micrometer level is an exciting unresolved problem. Here we consider diffusion transverse to a bundle of fibers, and show theoretically, as well as using Monte Carlo simulations and measurements in a phantom made of parallel fibers mimicking axons, that the time dependent diffusion coefficient approaches its macroscopic limit slowly, in a (ln t)/t fashion. The logarithmic singularity arises due to short range disorder in the fiber packing. We identify short range disorder in axonal fibers based on histological data from the splenium, and argue that the time dependent contribution to the overall diffusion coefficient from the extra-axonal water dominates that of the intra-axonal water. This dominance may explain the bias in measuring axon diameters in clinical settings. The short range disorder is also reflected in the asymptotically linear frequency dependence of the diffusion coefficient measured with oscillating gradients, in agreement with recent experiments. Our results relate the measured diffusion to the mesoscopic structure of neuronal tissue, uncovering the sensitivity of diffusion metrics to axonal arrangement within a fiber tract, and providing an alternative interpretation of axonal diameter mapping techniques.

  15. Quantum Coherence and Random Fields at Mesoscopic Scales

    SciTech Connect

    Rosenbaum, Thomas F.

    2016-03-01

    We seek to explore and exploit model, disordered and geometrically frustrated magnets where coherent spin clusters stably detach themselves from their surroundings, leading to extreme sensitivity to finite frequency excitations and the ability to encode information. Global changes in either the spin concentration or the quantum tunneling probability via the application of an external magnetic field can tune the relative weights of quantum entanglement and random field effects on the mesoscopic scale. These same parameters can be harnessed to manipulate domain wall dynamics in the ferromagnetic state, with technological possibilities for magnetic information storage. Finally, extensions from quantum ferromagnets to antiferromagnets promise new insights into the physics of quantum fluctuations and effective dimensional reduction. A combination of ac susceptometry, dc magnetometry, noise measurements, hole burning, non-linear Fano experiments, and neutron diffraction as functions of temperature, magnetic field, frequency, excitation amplitude, dipole concentration, and disorder address issues of stability, overlap, coherence, and control. We have been especially interested in probing the evolution of the local order in the progression from spin liquid to spin glass to long-range-ordered magnet.

  16. Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory.

    PubMed

    Ge, Hao; Qian, Hong

    2016-11-01

    Gibbs' macroscopic chemical thermodynamics is one of the most important theories in chemistry. Generalizing it to mesoscaled nonequilibrium systems is essential to biophysics. The nonequilibrium stochastic thermodynamics of chemical reaction kinetics suggested a free energy balance equation dF^{(meso)}/dt=E_{in}-e_{p} in which the free energy input rate E_{in} and dissipation rate e_{p} are both non-negative, and E_{in}≤e_{p}. We prove that in the macroscopic limit by merely allowing the molecular numbers to be infinite, the generalized mesoscopic free energy F^{(meso)} converges to φ^{ss}, the large deviation rate function for the stationary distributions. This generalized macroscopic free energy φ^{ss} now satisfies a balance equation dφ^{ss}(x)/dt=cmf(x)-σ(x), in which x represents chemical concentration. The chemical motive force cmf(x) and entropy production rate σ(x) are both non-negative, and cmf(x)≤σ(x). The balance equation is valid generally in isothermal driven systems and is different from mechanical energy conservation and the first law; it is actually an unknown form of the second law. Consequences of the emergent thermodynamic quantities and equalities are further discussed. The emergent "law" is independent of underlying kinetic details. Our theory provides an example showing how a macroscopic law emerges from a level below.

  17. Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory

    NASA Astrophysics Data System (ADS)

    Ge, Hao; Qian, Hong

    2016-11-01

    Gibbs' macroscopic chemical thermodynamics is one of the most important theories in chemistry. Generalizing it to mesoscaled nonequilibrium systems is essential to biophysics. The nonequilibrium stochastic thermodynamics of chemical reaction kinetics suggested a free energy balance equation d F(meso)/d t =Ein-ep in which the free energy input rate Ein and dissipation rate ep are both non-negative, and Ein≤ep . We prove that in the macroscopic limit by merely allowing the molecular numbers to be infinite, the generalized mesoscopic free energy F(meso) converges to φss, the large deviation rate function for the stationary distributions. This generalized macroscopic free energy φss now satisfies a balance equation d φss(x ) /d t =cmf(x ) -σ (x ) , in which x represents chemical concentration. The chemical motive force cmf(x ) and entropy production rate σ (x ) are both non-negative, and cmf(x )≤σ (x ) . The balance equation is valid generally in isothermal driven systems and is different from mechanical energy conservation and the first law; it is actually an unknown form of the second law. Consequences of the emergent thermodynamic quantities and equalities are further discussed. The emergent "law" is independent of underlying kinetic details. Our theory provides an example showing how a macroscopic law emerges from a level below.

  18. Mesoscopic structure formation in condensed matter due to vacuum fluctuations

    NASA Astrophysics Data System (ADS)

    Sen, Siddhartha; Gupta, Kumar S.; Coey, J. M. D.

    2015-10-01

    An observable influence of zero-point fluctuations of the vacuum electromagnetic field on bound electrons is well known in the hydrogen atom, where it produces the Lamb shift. Here, we adapt an approach used to explain the Lamb shift in terms of a slight expansion of the orbits due to interaction with the zero-point field and apply it to assemblies of N electrons that are modeled as independent atomically bound two-level systems. The effect is to stabilize a collective ground-state energy, which leads to a prediction of novel effects at room temperature for quasi-two-dimensional systems over a range of parameters in the model, namely, N , the two-level excitation energy ℏ ω and the ionization energy ℏ ω +ɛ . Some mesoscopic systems where these effects may be observable include water sheaths on protein or DNA, surfaces of gaseous nanobubbles, and the magnetic response of inhomogeneous, electronically dilute oxides. No such effects are envisaged for uniform three-dimensional systems.

  19. Electron-photon coupling in mesoscopic quantum electrodynamics

    NASA Astrophysics Data System (ADS)

    Cottet, A.; Kontos, T.; Douçot, B.

    2015-05-01

    Understanding the interaction between cavity photons and electronic nanocircuits is crucial for the development of mesoscopic quantum electrodynamics (QED). One has to combine ingredients from atomic cavity QED, such as orbital degrees of freedom, with tunneling physics and strong cavity field inhomogeneities, specific to superconducting circuit QED. It is therefore necessary to introduce a formalism which bridges between these two domains. We develop a general method based on a photonic pseudopotential to describe the electric coupling between electrons in a nanocircuit and cavity photons. In this picture, photons can induce simultaneously orbital energy shifts, tunneling, and local orbital transitions. We study in detail the elementary example of a single quantum dot with a single normal metal reservoir, coupled to a cavity. Photon-induced tunneling terms lead to a nonuniversal relation between the cavity frequency pull and the damping pull. Our formalism can also be applied to multiple quantum dot circuits, molecular circuits, quantum point contacts, metallic tunnel junctions, and superconducting nanostructures enclosing Andreev bound states or Majorana bound states, for instance.

  20. Superparamagnetism-induced mesoscopic electron focusing in topological insulators

    NASA Astrophysics Data System (ADS)

    Sessi, P.; Rüßmann, P.; Bathon, T.; Barla, A.; Kokh, K. A.; Tereshchenko, O. E.; Fauth, K.; Mahatha, S. K.; Valbuena, M. A.; Godey, S.; Glott, F.; Mugarza, A.; Gargiani, P.; Valvidares, M.; Long, N. H.; Carbone, C.; Mavropoulos, P.; Blügel, S.; Bode, M.

    2016-08-01

    Recently it has been shown that surface magnetic doping of topological insulators induces backscattering of Dirac states which are usually protected by time-reversal symmetry [Sessi et al., Nat. Commun. 5, 5349 (2014), 10.1038/ncomms6349]. Here we report on quasiparticle interference measurements where, by improved Fermi level tuning, strongly focused interference patterns on surface Mn-doped Bi2Te3 could be directly observed by means of scanning tunneling microscopy at 4 K. Ab initio and model calculations reveal that their mesoscopic coherence relies on two prerequisites: (i) a hexagonal Fermi surface with large parallel segments (nesting) and (ii) magnetic dopants which couple to a high-spin state. Indeed, x-ray magnetic circular dichroism shows superparamagnetism even at very dilute Mn concentrations. Our findings provide evidence of strongly anisotropic Dirac-fermion-mediated interactions and demonstrate how spin information can be transmitted over long distances, allowing the design of experiments and devices based on coherent quantum effects in topological insulators.

  1. The circuit architecture of whole brains at the mesoscopic scale.

    PubMed

    Mitra, Partha P

    2014-09-17

    Vertebrate brains of even moderate size are composed of astronomically large numbers of neurons and show a great degree of individual variability at the microscopic scale. This variation is presumably the result of phenotypic plasticity and individual experience. At a larger scale, however, relatively stable species-typical spatial patterns are observed in neuronal architecture, e.g., the spatial distributions of somata and axonal projection patterns, probably the result of a genetically encoded developmental program. The mesoscopic scale of analysis of brain architecture is the transitional point between a microscopic scale where individual variation is prominent and the macroscopic level where a stable, species-typical neural architecture is observed. The empirical existence of this scale, implicit in neuroanatomical atlases, combined with advances in computational resources, makes studying the circuit architecture of entire brains a practical task. A methodology has previously been proposed that employs a shotgun-like grid-based approach to systematically cover entire brain volumes with injections of neuronal tracers. This methodology is being employed to obtain mesoscale circuit maps in mouse and should be applicable to other vertebrate taxa. The resulting large data sets raise issues of data representation, analysis, and interpretation, which must be resolved. Even for data representation the challenges are nontrivial: the conventional approach using regional connectivity matrices fails to capture the collateral branching patterns of projection neurons. Future success of this promising research enterprise depends on the integration of previous neuroanatomical knowledge, partly through the development of suitable computational tools that encapsulate such expertise.

  2. A source to deliver mesoscopic particles for laser plasma studies.

    PubMed

    Gopal, R; Kumar, R; Anand, M; Kulkarni, A; Singh, D P; Krishnan, S R; Sharma, V; Krishnamurthy, M

    2017-02-01

    Intense ultrashort laser produced plasmas are a source for high brightness, short burst of X-rays, electrons, and high energy ions. Laser energy absorption and its disbursement strongly depend on the laser parameters and also on the initial size and shape of the target. The ability to change the shape, size, and material composition of the matter that absorbs light is of paramount importance not only from a fundamental physics point of view but also for potentially developing laser plasma sources tailored for specific applications. The idea of preparing mesoscopic particles of desired size/shape and suspending them in vacuum for laser plasma acceleration is a sparsely explored domain. In the following report we outline the development of a delivery mechanism of microparticles into an effusive jet in vacuum for laser plasma studies. We characterise the device in terms of particle density, particle size distribution, and duration of operation under conditions suitable for laser plasma studies. We also present the first results of x-ray emission from micro crystals of boric acid that extends to 100 keV even under relatively mild intensities of 10(16) W/cm(2).

  3. Mesoscopic structure of neuronal tracts from time-dependent diffusion

    PubMed Central

    Burcaw, Lauren M.; Fieremans, Els; Novikov, Dmitry S.

    2015-01-01

    Interpreting brain diffusion MRI measurements in terms of neuronal structure at a micrometer level is an exciting unresolved problem. Here we consider diffusion transverse to a bundle of fibers, and show theoretically, as well as using Monte Carlo simulations and measurements in a phantom made of parallel fibers mimicking axons, that the time dependent diffusion coefficient approaches its macroscopic limit slowly, in a (lnt)/t fashion. The logarithmic singularity arises due to short range disorder in the fiber packing. We identify short range disorder in axonal fibers based on histological data from the splenium, and argue that the time dependent contribution to the overall diffusion coefficient from the extra-axonal water dominates that of the intra-axonal water. This dominance may explain the bias in measuring axon diameters in clinical settings. The short range disorder is also reflected in the linear frequency dependence of the diffusion coefficient measured with oscillating gradients, in agreement with recent experiments. Our results relate the measured diffusion to the mesoscopic structure of neuronal tissue, uncovering the sensitivity of diffusion metrics to axonal arrangement within a fiber tract, and providing an alternative interpretation of axonal diameter mapping techniques. PMID:25837598

  4. Analysing DNA structural parameters using a mesoscopic model

    NASA Astrophysics Data System (ADS)

    Amarante, Tauanne D.; Weber, Gerald

    2014-03-01

    The Peyrard-Bishop model is a mesoscopic approximation to model DNA and RNA molecules. Several variants of this model exists, from 3D Hamiltonians, including torsional angles, to simpler 2D versions. Currently, we are able to parametrize the 2D variants of the model which allows us to extract important information about the molecule. For example, with this technique we were able recently to obtain the hydrogen bonds of RNA from melting temperatures, which previously were obtainable only from NMR measurements. Here, we take the 3D torsional Hamiltonian and set the angles to zero. Curiously, in doing this we do not recover the traditional 2D Hamiltonians. Instead, we obtain a different 2D Hamiltonian which now includes a base pair step distance, commonly known as rise. A detailed knowledge of the rise distance is important as it determines the overall length of the DNA molecule. This 2D Hamiltonian provides us with the exciting prospect of obtaining DNA structural parameters from melting temperatures. Our results of the rise distance at low salt concentration are in good qualitative agreement with those from several published x-ray measurements. We also found an important dependence of the rise distance with salt concentration. In contrast to our previous calculations, the elastic constants now show little dependence with salt concentrations which appears to be closer to what is seen experimentally in DNA flexibility experiments.

  5. PRATHAM: Parallel Thermal Hydraulics Simulations using Advanced Mesoscopic Methods

    SciTech Connect

    Joshi, Abhijit S; Jain, Prashant K; Mudrich, Jaime A; Popov, Emilian L

    2012-01-01

    At the Oak Ridge National Laboratory, efforts are under way to develop a 3D, parallel LBM code called PRATHAM (PaRAllel Thermal Hydraulic simulations using Advanced Mesoscopic Methods) to demonstrate the accuracy and scalability of LBM for turbulent flow simulations in nuclear applications. The code has been developed using FORTRAN-90, and parallelized using the message passing interface MPI library. Silo library is used to compact and write the data files, and VisIt visualization software is used to post-process the simulation data in parallel. Both the single relaxation time (SRT) and multi relaxation time (MRT) LBM schemes have been implemented in PRATHAM. To capture turbulence without prohibitively increasing the grid resolution requirements, an LES approach [5] is adopted allowing large scale eddies to be numerically resolved while modeling the smaller (subgrid) eddies. In this work, a Smagorinsky model has been used, which modifies the fluid viscosity by an additional eddy viscosity depending on the magnitude of the rate-of-strain tensor. In LBM, this is achieved by locally varying the relaxation time of the fluid.

  6. Mesoscopic fast ion conduction in nanometre-scale planar heterostructures

    NASA Astrophysics Data System (ADS)

    Sata, N.; Eberman, K.; Eberl, K.; Maier, J.

    2000-12-01

    Ion conduction is of prime importance for solid-state reactions in ionic systems, and for devices such as high-temperature batteries and fuel cells, chemical filters and sensors. Ionic conductivity in solid electrolytes can be improved by dissolving appropriate impurities into the structure or by introducing interfaces that cause the redistribution of ions in the space-charge regions. Heterojunctions in two-phase systems should be particularly efficient at improving ionic conduction, and a qualitatively different conductivity behaviour is expected when interface spacing is comparable to or smaller than the width of the space-charge regions in comparatively large crystals. Here we report the preparation, by molecular-beam epitaxy, of defined heterolayered films composed of CaF2 and BaF2 that exhibit ionic conductivity (parallel to the interfaces) increasing proportionally with interface density-for interfacial spacing greater than 50 nanometres. The results are in excellent agreement with semi-infinite space-charge calculations, assuming a redistribution of fluoride ions at the interfaces. If the spacing is reduced further, the boundary zones overlap and the predicted mesoscopic size effect is observed. At this point, the single layers lose their individuality and an artificial ionically conducting material with anomalous transport properties is generated. Our results should lead to fundamental insight into ionic contact processes and to tailored ionic conductors of potential relevance for medium-temperature applications.

  7. Wetting of mesoscopic soft cylinders: Structure and layering transitions

    NASA Astrophysics Data System (ADS)

    Ahrens, Heiko; Hugenberg, Norbert; Schmidt, Manfred; Helm, Christiane A.

    1999-10-01

    The wetting of soft mesoscopic long-chain particles is studied. As a model system, a cylindrical brush with poly(vinyl)pyridine side chains on the water surface is characterized by isotherms and x-ray reflectivity. The forces from the two planar interfaces and the intra- and interparticle interactions are all of comparable magnitude. Two layering transitions occur, one from the monolayer to the double layer, the next to a homogeneous multilayer. The hard wall from which layering starts is the smooth polymer/air interface. Indeed, they particles in the top layer of both the double- and the multilayer have their cylinder axis parallel to the surface and are laterally compressed. In contrast, the polymer/water interface is diffuse due to brush swelling. Generally, the long-chain particles adjacent to the respective interfaces do not maintain their circular diameters. The thickness of the monolayer can be varied by a factor 3.5, up to 53 Å. An additional phase transition occurs within the monolayer, which is attributed to a change of the side chains from a flattened to a compressed state at constant volume. Atmoic force microscope images of the monolayer transferred onto a solid indicate local cylinder alignment.

  8. A source to deliver mesoscopic particles for laser plasma studies

    NASA Astrophysics Data System (ADS)

    Gopal, R.; Kumar, R.; Anand, M.; Kulkarni, A.; Singh, D. P.; Krishnan, S. R.; Sharma, V.; Krishnamurthy, M.

    2017-02-01

    Intense ultrashort laser produced plasmas are a source for high brightness, short burst of X-rays, electrons, and high energy ions. Laser energy absorption and its disbursement strongly depend on the laser parameters and also on the initial size and shape of the target. The ability to change the shape, size, and material composition of the matter that absorbs light is of paramount importance not only from a fundamental physics point of view but also for potentially developing laser plasma sources tailored for specific applications. The idea of preparing mesoscopic particles of desired size/shape and suspending them in vacuum for laser plasma acceleration is a sparsely explored domain. In the following report we outline the development of a delivery mechanism of microparticles into an effusive jet in vacuum for laser plasma studies. We characterise the device in terms of particle density, particle size distribution, and duration of operation under conditions suitable for laser plasma studies. We also present the first results of x-ray emission from micro crystals of boric acid that extends to 100 keV even under relatively mild intensities of 1016 W/cm2.

  9. Mesoscopic architectures of porous coordination polymers fabricated by pseudomorphic replication.

    PubMed

    Reboul, Julien; Furukawa, Shuhei; Horike, Nao; Tsotsalas, Manuel; Hirai, Kenji; Uehara, Hiromitsu; Kondo, Mio; Louvain, Nicolas; Sakata, Osami; Kitagawa, Susumu

    2012-06-24

    The spatial organization of porous coordination polymer (PCP) crystals into higher-order structures is critical for their integration into separation systems, heterogeneous catalysts, ion/electron transport and photonic devices. Here, we demonstrate a rapid method to spatially control the nucleation site, leading to the formation of mesoscopic architecture made of PCPs, in both two and three dimensions. Inspired by geological processes, this method relies on the morphological replacement of a shaped sacrificial metal oxide used both as a metal source and as an 'architecture-directing agent' by an analogous PCP architecture. Spatiotemporal harmonization of the metal oxide dissolution and the PCP crystallization allowed the preservation of very fine mineral morphological details of periodic alumina inverse opal structures. The replication of randomly structured alumina aerogels resulted in a PCP architecture with hierarchical porosity in which the hydrophobic micropores of the PCP and the mesopores/macropores inherited from the parent aerogels synergistically enhanced the material's selectivity and mass transfer for water/ethanol separation.

  10. Quantum spectra of Raman photon pairs from a mesoscopic particle

    NASA Astrophysics Data System (ADS)

    Ooi, C. H. Raymond; Loh, W. M. Edmund; Kam, C. H.

    2015-06-01

    Quantum Langevin formalism with noise operators is used to provide quantum descriptions of photon pairs (the Stokes and anti-Stokes fields) emitted by a mesoscopic spherical particle composed of quantum particles in a double Raman configuration. The spectra of the fields obtained are sensitive to the dimension of the microsphere and can be controlled by pump and control laser fields. Spectral peaks due to quantum coherence are Stark shifted by the laser fields experiencing autofocusing inside the spherical particle, causing broadening of peaks as the size of the microsphere increases. The antinormal-order spectrum is found to be identical to the normal-order spectrum. The anti-Stokes spectrum is identical to the Stokes spectrum when the linear dispersion is neglected. Frequency-dependent dielectric functions of the Stokes and anti-Stokes spectra corresponding to the linear dispersions of the particle yield narrow morphology-dependent resonance gain peaks at certain frequencies of the Stokes and anti-Stokes spectra that depend not only on the particle size but also on the angle of observation.

  11. The Circuit Architecture of Whole Brains at the Mesoscopic Scale

    PubMed Central

    Mitra, Partha P.

    2014-01-01

    Vertebrate brains of even moderate size are composed of astronomically large numbers of neurons and show a great degree of individual variability at the microscopic scale. This variation is presumably the result of phenotypic plasticity and individual experience. At a larger scale, however, relatively stable species-typical spatial patterns are observed in neuronal architecture, e.g., the spatial distributions of somata and axonal projection patterns, probably the result of a genetically encoded developmental program. The mesoscopic scale of analysis of brain architecture is the transitional point between a microscopic scale where individual variation is prominent and the macroscopic level where a stable, species-typical neural architecture is observed. The empirical existence of this scale, implicit in neuroanatomical atlases, combined with advances in computational resources, makes studying the circuit architecture of entire brains a practical task. A methodology has previously been proposed that employs a shotgun-like grid-based approach to systematically cover entire brain volumes with injections of neuronal tracers. This methodology is being employed to obtain mesoscale circuit maps in mouse and should be applicable to other vertebrate taxa. The resulting large data sets raise issues of data representation, analysis, and interpretation, which must be resolved. Even for data representation the challenges are nontrivial: the conventional approach using regional connectivity matrices fails to capture the collateral branching patterns of projection neurons. Future success of this promising research enterprise depends on the integration of previous neuroanatomical knowledge, partly through the development of suitable computational tools that encapsulate such expertise. PMID:25233311

  12. Energy transfer in mesoscopic vibrational systems enabled by eigenfrequency fluctuations

    NASA Astrophysics Data System (ADS)

    Atalaya, Juan

    Energy transfer between low-frequency vibrational modes can be achieved by means of nonlinear coupling if their eigenfrequencies fulfill certain nonlinear resonance conditions. Because of the discreteness of the vibrational spectrum at low frequencies, such conditions may be difficult to satisfy for most low-frequency modes in typical mesoscopic vibrational systems. Fluctuations of the vibrational eigenfrequencies can also be relatively strong in such systems. We show that energy transfer between modes can occur in the absence of nonlinear resonance if frequency fluctuations are allowed. The case of three modes with cubic nonlinear coupling and no damping is particularly interesting. It is found that the system has a non-thermal equilibrium state which depends only on the initial conditions. The rate at which the system approaches to such state is determined by the parameters such as the noise strength and correlation time, the nonlinearity strength and the detuning from exact nonlinear resonance. We also discuss the case of many weakly coupled modes. Our results shed light on the problem of energy relaxation of low-frequency vibrational modes into the continuum of high-frequency vibrational modes. The results have been obtained with Mark Dykman. Alternative email: jatalaya2012@gmail.com.

  13. Unraveling the Structure of Ultracold Mesoscopic Collinear Molecular Ions

    NASA Astrophysics Data System (ADS)

    Schurer, J. M.; Negretti, A.; Schmelcher, P.

    2017-08-01

    We present an in-depth many-body investigation of the so-called mesoscopic molecular ions that can buildup when an ion is immersed into an atomic Bose-Einstein condensate in one dimension. To this end, we employ the multilayer multiconfiguration time-dependent Hartree method for mixtures of ultracold bosonic species for solving the underlying many-body Schrödinger equation. This enables us to unravel the actual structure of such massive charged molecules from a microscopic perspective. Laying out their phase diagram with respect to atom number and interatomic interaction strength, we determine the maximal number of atoms bound to the ion and reveal spatial densities and molecular properties. Interestingly, we observe a strong interaction-induced localization, especially for the ion, that we explain by the generation of a large effective mass, similarly to ions in liquid Helium. Finally, we predict the dynamical response of the ion to small perturbations. Our results provide clear evidence for the importance of quantum correlations, as we demonstrate by benchmarking them with wave function ansatz classes employed in the literature.

  14. Universality of Shot Noise in Mesoscopic Diffusive Conductors.

    NASA Astrophysics Data System (ADS)

    Sukhorukov, Eugene; Loss, Daniel

    1998-03-01

    Shot noise is the time-dependent fluctuations in the electrical current caused by the discreteness of the electron charge. In mesoscopic conductors the shot noise is suppressed below the noise of a Poisson process due to correlations in the electron transmission imposed by the Pauli principle. In diffusive conductors with purely elastic scattering the suppression factor is 1/3, and in the case of strong electron-electron scattering it is √3/4 (C.W.J. Beenakker and M. Büttiker, Phys. Rev. B46, 1889 (1992); K.E. Nagaev, Phys. Lett. A169, 103 (1992); Phys. Rev. B52, 4740 (1995)). Subsequently, it has been proven by Nazarov that the 1/3 suppression is universal and holds for an arbitrary two-terminal geometry of the conductor and distribution of impurities. Using a different approach, we confirm the universality of the 1/3 and prove the universality of the √3/4 suppressions. A possible generalization of our results to the case of multiterminal conductors is discussed.

  15. In vitro testing of biological control agents on A1 and A2 isolates of Phytophthora ramorum

    Treesearch

    Marianne Elliott; Simon Shamoun

    2008-01-01

    Biological control products were tested in vitro with six isolates of Phytophthora ramorum. These isolates were geographically diverse and were selected based on their pathogenicity to detached Rhododendron leaves. In addition to five commercially available biocontrol products, nine species of Trichoderma were tested. The in vitro...

  16. The Athlete Biological Passport: How to Personalize Anti-Doping Testing across an Athlete's Career?

    PubMed

    Robinson, Neil; Sottas, Pierre-Edouard; Schumacher, Yorck Olaf

    2017-01-01

    For decades, drug testing has been the main instrument at the disposal of anti-doping authorities. The availability in the 1980s of substances identical to those produced by the human body, including the "big 3" (erythropoietin, testosterone, and growth hormone), necessitated a new paradigm in anti-doping. The athlete biological passport (ABP) is a new paradigm, complementary to traditional drug testing, based on the personalized monitoring of doping biomarkers. Athletes who abuse doping substances do so to trigger physiological changes that provide performance enhancement. The ABP aims to detect these changes through its 3 hematological, steroidal, and endocrine modules. Any deviation of a biomarker from what is expected in a healthy physiological condition can be attributable to doping or a medical condition, which, interestingly, is also the criterion used to define a banned substance. Recent advances in proteomics and metabolomics offer immense opportunities to enhance the ABP. The ABP shares multiple aspects with the present customization of health care and personalized medicine. © 2017 S. Karger AG, Basel.

  17. Testing surrogacy assumptions: can threatened and endangered plants be grouped by biological similarity and abundances?

    PubMed

    Che-Castaldo, Judy P; Neel, Maile C

    2012-01-01

    There is renewed interest in implementing surrogate species approaches in conservation planning due to the large number of species in need of management but limited resources and data. One type of surrogate approach involves selection of one or a few species to represent a larger group of species requiring similar management actions, so that protection and persistence of the selected species would result in conservation of the group of species. However, among the criticisms of surrogate approaches is the need to test underlying assumptions, which remain rarely examined. In this study, we tested one of the fundamental assumptions underlying use of surrogate species in recovery planning: that there exist groups of threatened and endangered species that are sufficiently similar to warrant similar management or recovery criteria. Using a comprehensive database of all plant species listed under the U.S. Endangered Species Act and tree-based random forest analysis, we found no evidence of species groups based on a set of distributional and biological traits or by abundances and patterns of decline. Our results suggested that application of surrogate approaches for endangered species recovery would be unjustified. Thus, conservation planning focused on individual species and their patterns of decline will likely be required to recover listed species.

  18. Future Food Production System Development Pulling from Space Biology Crop Growth Testing in Veggie

    NASA Technical Reports Server (NTRS)

    Massa, G. D.; Romeyn, M. W.; Fritsche, R. F.

    2017-01-01

    lessons, as we learn about growing at different scales and move toward developing systems that require less launch mass. Veggie will be used as a test bed for novel food production technologies. Veggie is a relatively simple precursor food production system but the knowledge gained from space biology validation tests in Veggie will have far reaching repercussions on future exploration food production.

  19. Epistemological Predictors of "Self Efficacy on Learning Biology" and "Test Anxiety Related to Evaluation of Learning on Biology" for Pre-service Elementary Teachers

    NASA Astrophysics Data System (ADS)

    Köksal, Mustafa Serdar

    2011-11-01

    The degree to which pre-service teachers learn biology is related to both motivational factors of self-regulation and factors regarding epistemological beliefs. At the same time, self-regulation and epistemological beliefs are also associated with one another. Based on this relationship, the purpose of this study was to investigate the relationship between components of epistemological beliefs and self-refulation (self-efficacy and test-anxiety) on learning biology. The study was conducted with 411 pre-service elementary and pre-service elementary science teachers by using a predictive research approach. Collected data was analyzed by the multiple linear regression technique. The results showed that only the belief about "existence of one truth" was a significant predictor of test anxiety while there was no epistemological predictor of self-efficacy. Conclusions and implications of the study will be discussed.

  20. An Ultra-Wideband Cross-Correlation Radiometer for Mesoscopic Experiments

    NASA Astrophysics Data System (ADS)

    Toonen, Ryan; Haselby, Cyrus; Qin, Hua; Eriksson, Mark; Blick, Robert

    2007-03-01

    We have designed, built and tested a cross-correlation radiometer for detecting statistical order in the quantum fluctuations of mesoscopic experiments at sub-Kelvin temperatures. Our system utilizes a fully analog front-end--operating over the X- and Ku-bands (8 to 18 GHz)--for computing the cross-correlation function. Digital signal processing techniques are used to provide robustness against instrumentation drifts and offsets. The economized version of our instrument can measure, with sufficient correlation efficiency, noise signals having power levels as low as 10 fW. We show that, if desired, we can improve this performance by including cryogenic preamplifiers which boost the signal-to-noise ratio near the signal source. By adding a few extra components, we can measure both the real and imaginary parts of the cross-correlation function--improving the overall signal-to-noise ratio by a factor of sqrt[2]. We demonstrate the utility of our cross-correlator with noise power measurements from a quantum point contact.

  1. Novel Biological Approaches for Testing the Contributions of Single DSBs and DSB Clusters to the Biological Effects of High LET Radiation

    PubMed Central

    Mladenova, Veronika; Mladenov, Emil; Iliakis, George

    2016-01-01

    The adverse biological effects of ionizing radiation (IR) are commonly attributed to the generation of DNA double-strand breaks (DSBs). IR-induced DSBs are generated by clusters of ionizations, bear damaged terminal nucleotides, and frequently comprise base damages and single-strand breaks in the vicinity generating a unique DNA damage-clustering effect that increases DSB “complexity.” The number of ionizations in clusters of different radiation modalities increases with increasing linear energy transfer (LET), and is thought to determine the long-known LET-dependence of the relative biological effectiveness (RBE). Multiple ionizations may also lead to the formation of DSB clusters, comprising two or more DSBs that destabilize chromatin further and compromise overall processing. DSB complexity and DSB-cluster formation are increasingly considered in the development of mathematical models of radiation action, which are then “tested” by fitting available experimental data. Despite a plethora of such mathematical models the ultimate goal, i.e., the “a priori” prediction of the radiation effect, has not yet been achieved. The difficulty partly arises from unsurmountable difficulties in testing the fundamental assumptions of such mathematical models in defined biological model systems capable of providing conclusive answers. Recently, revolutionary advances in methods allowing the generation of enzymatic DSBs at random or in well-defined locations in the genome, generate unique testing opportunities for several key assumptions frequently fed into mathematical modeling – including the role of DSB clusters in the overall effect. Here, we review the problematic of DSB-cluster formation in radiation action and present novel biological technologies that promise to revolutionize the way we address the biological consequences of such lesions. We describe new ways of exploiting the I-SceI endonuclease to generate DSB-clusters at random locations in the genome and

  2. Dosimetric and biological results from the Bacillus subtilis Biostack experiment with the Apollo-Soyuz Test Project.

    PubMed

    Facius, R; Bucker, H; Horneck, G; Reitz, G; Schafer, M

    1979-01-01

    The evaluation of the Bacillus subtilis experiment has been completed. The biological and the physical results for this part of the Apollo-Soyuz Test Project (ASTP) Biostack experiment are given. This comprises dosimetric data for the cosmic radiation at that orbit as well as biological findings from two types of plastic detectors. Further, the frequency distributions of the physical quantities atomic number, energy and energy loss of the heavy ions within the sample of spores hit are presented. The biological hazard presented by cosmic HZE-particles has been much underestimated.

  3. Test Results of Level A Suits to Challenge by Chemical and Biological Warfare Agents and Simulants: Summary Report

    DTIC Science & Technology

    1998-06-01

    Agent Permeation of GB and HD Through 25-Mil Chemical Protective Glove 30 3.3 System Test (Aerosol Simulant) 3.3.1 System Test (Aerosol Simulant... Chemical Protective Glove GB Permeation 176 Appendix Q: Commander Brigade F91 Table Q - 3: Commander Brigade F91: System Test (Vapor Simulant) Results No...capability to protect in a chemical agent or biological agent environment. Each

  4. Hearing Tests on Mobile Devices: Evaluation of the Reference Sound Level by Means of Biological Calibration

    PubMed Central

    Kipiński, Lech; Grysiński, Tomasz; Kręcicki, Tomasz

    2016-01-01

    Background Hearing tests carried out in home setting by means of mobile devices require previous calibration of the reference sound level. Mobile devices with bundled headphones create a possibility of applying the predefined level for a particular model as an alternative to calibrating each device separately. Objective The objective of this study was to determine the reference sound level for sets composed of a mobile device and bundled headphones. Methods Reference sound levels for Android-based mobile devices were determined using an open access mobile phone app by means of biological calibration, that is, in relation to the normal-hearing threshold. The examinations were conducted in 2 groups: an uncontrolled and a controlled one. In the uncontrolled group, the fully automated self-measurements were carried out in home conditions by 18- to 35-year-old subjects, without prior hearing problems, recruited online. Calibration was conducted as a preliminary step in preparation for further examination. In the controlled group, audiologist-assisted examinations were performed in a sound booth, on normal-hearing subjects verified through pure-tone audiometry, recruited offline from among the workers and patients of the clinic. In both the groups, the reference sound levels were determined on a subject’s mobile device using the Bekesy audiometry. The reference sound levels were compared between the groups. Intramodel and intermodel analyses were carried out as well. Results In the uncontrolled group, 8988 calibrations were conducted on 8620 different devices representing 2040 models. In the controlled group, 158 calibrations (test and retest) were conducted on 79 devices representing 50 models. Result analysis was performed for 10 most frequently used models in both the groups. The difference in reference sound levels between uncontrolled and controlled groups was 1.50 dB (SD 4.42). The mean SD of the reference sound level determined for devices within the same model

  5. Hearing Tests on Mobile Devices: Evaluation of the Reference Sound Level by Means of Biological Calibration.

    PubMed

    Masalski, Marcin; Kipiński, Lech; Grysiński, Tomasz; Kręcicki, Tomasz

    2016-05-30

    Hearing tests carried out in home setting by means of mobile devices require previous calibration of the reference sound level. Mobile devices with bundled headphones create a possibility of applying the predefined level for a particular model as an alternative to calibrating each device separately. The objective of this study was to determine the reference sound level for sets composed of a mobile device and bundled headphones. Reference sound levels for Android-based mobile devices were determined using an open access mobile phone app by means of biological calibration, that is, in relation to the normal-hearing threshold. The examinations were conducted in 2 groups: an uncontrolled and a controlled one. In the uncontrolled group, the fully automated self-measurements were carried out in home conditions by 18- to 35-year-old subjects, without prior hearing problems, recruited online. Calibration was conducted as a preliminary step in preparation for further examination. In the controlled group, audiologist-assisted examinations were performed in a sound booth, on normal-hearing subjects verified through pure-tone audiometry, recruited offline from among the workers and patients of the clinic. In both the groups, the reference sound levels were determined on a subject's mobile device using the Bekesy audiometry. The reference sound levels were compared between the groups. Intramodel and intermodel analyses were carried out as well. In the uncontrolled group, 8988 calibrations were conducted on 8620 different devices representing 2040 models. In the controlled group, 158 calibrations (test and retest) were conducted on 79 devices representing 50 models. Result analysis was performed for 10 most frequently used models in both the groups. The difference in reference sound levels between uncontrolled and controlled groups was 1.50 dB (SD 4.42). The mean SD of the reference sound level determined for devices within the same model was 4.03 dB (95% CI 3

  6. Mesoscopics of ultrasound and seismic waves: application to passive imaging

    NASA Astrophysics Data System (ADS)

    Larose, É.

    2006-05-01

    This manuscript deals with different aspects of the propagation of acoustic and seismic waves in heterogeneous media, both simply and multiply scattering ones. After a short introduction on conventional imaging techniques, we describe two observations that demonstrate the presence of multiple scattering in seismic records: the equipartition principle, and the coherent backscattering effect (Chap. 2). Multiple scattering is related to the mesoscopic nature of seismic and acoustic waves, and is a strong limitation for conventional techniques like medical or seismic imaging. In the following part of the manuscript (Chaps. 3 5), we present an application of mesoscopic physics to acoustic and seismic waves: the principle of passive imaging. By correlating records of ambient noise or diffuse waves obtained at two passive sensors, it is possible to reconstruct the impulse response of the medium as if a source was placed at one sensor. This provides the opportunity of doing acoustics and seismology without a source. Several aspects of this technique are presented here, starting with theoretical considerations and numerical simulations (Chaps. 3, 4). Then we present experimental applications (Chap. 5) to ultrasound (passive tomography of a layered medium) and to seismic waves (passive imaging of California, and the Moon, with micro-seismic noise). Physique mésoscopique des ultrasons et des ondes sismiques : application à l'imagerie passive. Cet article de revue rassemble plusieurs aspects fondamentaux et appliqués de la propagation des ondes acoustiques et élastiques dans les milieux hétérogènes, en régime de diffusion simple ou multiple. Après une introduction sur les techniques conventionelles d'imagerie sismique et ultrasonore, nous présentons deux expériences qui mettent en évidence la présence de diffusion multiple dans les enregistrements sismologiques : l'équipartition des ondes, et la rétrodiffusion cohérente (Chap. 2). La diffusion multiple des

  7. Transport studies of mesoscopic and magnetic topological insulators

    NASA Astrophysics Data System (ADS)

    Kandala, Abhinav

    Topological Insulators (TI) are a novel class of materials that are ideally insulating in the bulk, but have gapless, metallic states at the surface. These surface states have very exciting properties such as suppressed backscattering and spin-momentum locking, which are of great interest for research efforts towards dissipation-less electronics and spintronics. The popular thermo-electrics from the Bi chalcogenide family -- Bi2Se3 and Bi 2Te3 -- have been experimentally demonstrated to be promising candidate TI materials, and form the chosen material system for this dissertation research. The first part of this dissertation research focuses on low temperature magneto-transport measurements of mesoscopic topological insulator devices (Chapter 3). The top-down patterning of epitaxial thin films of Bi2Se 3 and Bi2Te3 (that are plagued with bulk conduction) is motivated, in part, by an effort to enhance the surface-to-volume ratio in mesoscopic channels. At cryogenic temperatures, transport measurements of these devices reveal periodic conductance fluctuations in straight channel devices, despite the lack of any explicit patterning of the TI film into a ring or a loop. A careful analysis of the surface morphology and comparison with the transport data then demonstrate that scattering off the edges of triangular plateaus at the surface leads to the creation of Aharonov-Bohm electronic orbits responsible for the periodicity. Another major focus of this dissertation work is on combining topological insulators with magnetism. This has been shown to open a gap in the surface states leading to possibilities of magnetic "gating" and the realization of dissipation-less transport at zero-field, amongst several other exotic quantum phenomena. In this dissertation, I present two different schemes for probing these effects in electrical transport devices -- interfacing with insulating ferromagnets (Chapter 4) and bulk magnetic doping (Chapter 5). In Chapter 4, I shall present the

  8. Evaluation of growth based rapid microbiological methods for sterility testing of vaccines and other biological products.

    PubMed

    Parveen, Seema; Kaur, Simleen; David, Selwyn A Wilson; Kenney, James L; McCormick, William M; Gupta, Rajesh K

    2011-10-19

    Most biological products, including vaccines, administered by the parenteral route are required to be tested for sterility at the final container and also at various stages during manufacture. The sterility testing method described in the Code of Federal Regulations (21 CFR 610.12) and the United States Pharmacopoeia (USP, Chapter <71>) is based on the observation of turbidity in liquid culture media due to growth of potential contaminants. We evaluated rapid microbiological methods (RMM) based on detection of growth 1) by adenosine triphosphate (ATP) bioluminescence technology (Rapid Milliflex(®) Detection System [RMDS]), and 2) by CO(2) monitoring technologies (BacT/Alert and the BACTEC systems), as alternate sterility methods. Microorganisms representing Gram negative, Gram positive, aerobic, anaerobic, spore forming, slow growing bacteria, yeast, and fungi were prepared in aliquots of Fluid A or a biological matrix (including inactivated influenza vaccines) to contain approximately 0.1, 1, 10 and 100 colony forming units (CFU) in an inoculum of 10 ml. These preparations were inoculated to the specific media required for the various methods: 1) fluid thioglycollate medium (FTM) and tryptic soy broth (TSB) of the compendial sterility method (both membrane filtration and direct inoculation); 2) tryptic soy agar (TSA), Sabouraud dextrose agar (SDA) and Schaedler blood agar (SBA) of the RMDS; 3) iAST and iNST media of the BacT/Alert system and 4) Standard 10 Aerobic/F and Standard Anaerobic/F media of the BACTEC system. RMDS was significantly more sensitive in detecting various microorganisms at 0.1CFU than the compendial methods (p<0.05), whereas the compendial membrane filtration method was significantly more sensitive than the BACTEC and BacT/Alert methods (p<0.05). RMDS detected all microorganisms significantly faster than the compendial method (p<0.05). BacT/Alert and BACTEC methods detected most microorganisms significantly faster than the compendial method

  9. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

    NASA Astrophysics Data System (ADS)

    Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

    2015-07-01

    We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.

  10. Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

    PubMed Central

    Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

    2015-01-01

    We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. PMID:26156459

  11. Examples of testing global identifiability of biological and biomedical models with the DAISY software.

    PubMed

    Saccomani, Maria Pia; Audoly, Stefania; Bellu, Giuseppina; D'Angiò, Leontina

    2010-04-01

    DAISY (Differential Algebra for Identifiability of SYstems) is a recently developed computer algebra software tool which can be used to automatically check global identifiability of (linear and) nonlinear dynamic models described by differential equations involving polynomial or rational functions. Global identifiability is a fundamental prerequisite for model identification which is important not only for biological or medical systems but also for many physical and engineering systems derived from first principles. Lack of identifiability implies that the parameter estimation techniques may not fail but any obtained numerical estimates will be meaningless. The software does not require understanding of the underlying mathematical principles and can be used by researchers in applied fields with a minimum of mathematical background. We illustrate the DAISY software by checking the a priori global identifiability of two benchmark nonlinear models taken from the literature. The analysis of these two examples includes comparison with other methods and demonstrates how identifiability analysis is simplified by this tool. Thus we illustrate the identifiability analysis of other two examples, by including discussion of some specific aspects related to the role of observability and knowledge of initial conditions in testing identifiability and to the computational complexity of the software. The main focus of this paper is not on the description of the mathematical background of the algorithm, which has been presented elsewhere, but on illustrating its use and on some of its more interesting features. DAISY is available on the web site http://www.dei.unipd.it/ approximately pia/.

  12. Biological impact assessment of nanomaterial used in nanomedicine. introduction to the NanoTEST project.

    PubMed

    Juillerat-Jeanneret, Lucienne; Dusinska, Maria; Fjellsbø, Lise Marie; Collins, Andrew R; Handy, Richard D; Riediker, Michael

    2015-05-01

    Therapeutic nanoparticles (NPs) are used in nanomedicine as drug carriers or imaging agents, providing increased selectivity/specificity for diseased tissues. The first NPs in nanomedicine were developed for increasing the efficacy of known drugs displaying dose-limiting toxicity and poor bioavailability and for enhancing disease detection. Nanotechnologies have gained much interest owing to their huge potential for applications in industry and medicine. It is necessary to ensure and control the biocompatibility of the components of therapeutic NPs to guarantee that intrinsic toxicity does not overtake the benefits. In addition to monitoring their toxicity in vitro, in vivo and in silico, it is also necessary to understand their distribution in the human body, their biodegradation and excretion routes and dispersion in the environment. Therefore, a deep understanding of their interactions with living tissues and of their possible effects in the human (and animal) body is required for the safe use of nanoparticulate formulations. Obtaining this information was the main aim of the NanoTEST project, and the goals of the reports collected together in this special issue are to summarise the observations and results obtained by the participating research teams and to provide methodological tools for evaluating the biological impact of NPs.

  13. Advances in design and testing of limited angle optical diffraction tomographysystem for biological applications

    NASA Astrophysics Data System (ADS)

    Kuś, A.; Makowski, P.; Kujawińska, M.

    2016-03-01

    Optical diffraction tomography has been steadily proving its potential to study one of the hot topics in modern cell biology -- 3D dynamic changes in cells' morphology represented with refractive index values. In this technique digital holography is combined with tomographic reconstruction and thus it is necessary to provide projections acquired at different viewing directions. Usually the Mach-Zehnder interferometer configuration is used and while the object beam performs scanning, the reference beam is in most cases stationary. This approach either limits possible scanning strategies or requires additional mechanical movement to be introduced in the reference beam. On the other hand, spiral or grid scanning is possible in alternative common-path or Michelson configurations. However, in this case there is no guarantee that a specimen is sparse enough for the object to interfere with an object-free part of the beam. In this paper we present a modified version of Mach-Zehnder interferometer-based tomographic microscope, in which both object and reference beam are subject to scanning using one scanning device only thus making any scanning scenario possible. This concept is realized with a custom-built optical system in the reference beam and is appropriate for mechanical as well as optical scanning. Usually, the tomographic reconstruction setups and algorithms are verified using a microsphere phantom, which is not enough to test the influence of the distribution of the projections. In this work we propose a more complex calibration object created using two-photon polymerization.

  14. Biological activities of dihydrodiols derived from two polycyclic hydrocarbons in rodent test systems.

    PubMed Central

    Chouroulinkov, I.; Gentil, A.; Tierney, B.; Grover, P. L.; Sims, P.

    1979-01-01

    Comparisons have been made between (a) the initiation of tumours in mouse skin, (b) the induction of hyperplasia and the suppression of sebaceous glands in mouse skin and (c) the induction of s.c. tumours in rats, by either benzo[a]pyrene or 7-methylbenz[a]anthracene and their related K-region and non-K-region dihydrodiols. Whilst the 3,4-dihydrodiol derived from 7-methylbenz[a]anthracene is more active than the hydrocarbon in initiating tumours in mouse skin (subsequently promoted by a phorbol ester) the 7,8-dihydrodiol of benzo[a]pyrene is very much less active than benzo[a]pyrene itself in the induction of hyperplasia or the suppression of sebaceous glands in mouse skin or in the induction of s.c. sarcomas in rats. Since much other evidence suggests that the 3,4-dihydrodiol of 7-methylbenz[a]anthracene and the 7,8-dihydrodiol of benzo[a]pyrene are the dihydrodiols involved, via the related vicinal diol-epoxides, in the metabolic activation of these hydrocarbons, mouse skin initiation-promotion experiments may be more useful for the identification of such diols than the other two in vivo tests for biological activity used here. PMID:444395

  15. Mesoscopic dynamics of diffusion-influenced enzyme kinetics

    NASA Astrophysics Data System (ADS)

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-01

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t^{-1/2} and t^{-3/2} power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

  16. Excess protons in mesoscopic water-acetone nanoclusters

    NASA Astrophysics Data System (ADS)

    Semino, Rocío; Martí, Jordi; Guàrdia, Elvira; Laria, Daniel

    2012-11-01

    We carried out molecular dynamics simulation experiments to examine equilibrium and dynamical characteristics of the solvation of excess protons in mesoscopic, [m:n] binary polar clusters comprising m = 50 water molecules and n = 6, 25, and 100 acetone molecules. Contrasting from what is found in conventional macroscopic phases, the characteristics of the proton solvation are dictated, to a large extent, by the nature of the concentration fluctuations prevailing within the clusters. At low acetone contents, the overall cluster morphology corresponds to a segregated aqueous nucleus coated by an external aprotic phase. Under these circumstances, the proton remains localized at the surface of the water core, in a region locally deprived from acetone molecules. At higher acetone concentrations, we found clear evidence of the onset of the mixing process. The cluster structures present aqueous domains with irregular shape, fully embedded within the acetone phase. Still, the proton remains coordinated to the aqueous phase, with its closest solvation shell composed exclusively by three water molecules. As the relative concentration of acetone increases, the time scales characterizing proton transfer events between neighboring water molecules show considerable retardations, stretching into the nanosecond time domain already for n ˜ 25. In water-rich aggregates, and similarly to what is found in the bulk, proton transfers are controlled by acetone/water exchange processes taking place at the second solvation shell of the proton. As a distinctive feature of the transfer mechanism, translocation pathways also include diffusive motions of the proton from the surface down into inner regions of the underlying water domain.

  17. Mesoscopic simulations of accelerated polymer drift in microfluidic capillaries

    NASA Astrophysics Data System (ADS)

    Berkenbos, A.; Lowe, C. P.

    2007-10-01

    We use a mesoscopic simulation technique to study the transport of polymers in dilute solution flowing through a cylindrical tube. The simulations use an explicit solvent model to include all the relevant hydrodynamic couplings and a coarse grained ideal chain model for the polymers (appropriate for systems near the theta temperature). For the interactions between the solvent and the tube wall we use a novel method that ensures continuity of the stress at the interface. We show that the results for the polymer drift velocity are independent of the degree of coarse graining. Further, for the case where the size of the chains is small but not negligible compared to the tube radius, our results are in excellent agreement with experiment. However, they also show that in this regime, the "accelerated" drift, relative to the average solvent flow velocity, is described by the steric effect of the tube wall excluding the polymer center of mass from sampling the full cross section of the tube. Hydrodynamic interactions have a negligible influence in this regime. Consequently, the agreement between experiment and theories that approximates the former but includes the latter is fortunate. When the undisturbed polymer radius approaches or exceeds the tube radius, the hydrodynamic interactions do have a significant effect. They reduce the drift velocity, in qualitative agreement with theoretical predictions. The accelerated drift still approaches the maximum value, one would expect based on a Poiseuille flow but more slowly than if one neglects hydrodynamics. Finally, we propose an empirical fit that accurately describes data in the intermediate regime.

  18. Mesoscopic kinetic Monte Carlo modeling of organic photovoltaic device characteristics

    NASA Astrophysics Data System (ADS)

    Kimber, Robin G. E.; Wright, Edward N.; O'Kane, Simon E. J.; Walker, Alison B.; Blakesley, James C.

    2012-12-01

    Measured mobility and current-voltage characteristics of single layer and photovoltaic (PV) devices composed of poly{9,9-dioctylfluorene-co-bis[N,N'-(4-butylphenyl)]bis(N,N'-phenyl-1,4-phenylene)diamine} (PFB) and poly(9,9-dioctylfluorene-co-benzothiadiazole) (F8BT) have been reproduced by a mesoscopic model employing the kinetic Monte Carlo (KMC) approach. Our aim is to show how to avoid the uncertainties common in electrical transport models arising from the need to fit a large number of parameters when little information is available, for example, a single current-voltage curve. Here, simulation parameters are derived from a series of measurements using a self-consistent “building-blocks” approach, starting from data on the simplest systems. We found that site energies show disorder and that correlations in the site energies and a distribution of deep traps must be included in order to reproduce measured charge mobility-field curves at low charge densities in bulk PFB and F8BT. The parameter set from the mobility-field curves reproduces the unipolar current in single layers of PFB and F8BT and allows us to deduce charge injection barriers. Finally, by combining these disorder descriptions and injection barriers with an optical model, the external quantum efficiency and current densities of blend and bilayer organic PV devices can be successfully reproduced across a voltage range encompassing reverse and forward bias, with the recombination rate the only parameter to be fitted, found to be 1×107 s-1. These findings demonstrate an approach that removes some of the arbitrariness present in transport models of organic devices, which validates the KMC as an accurate description of organic optoelectronic systems, and provides information on the microscopic origins of the device behavior.

  19. Mesoscopic coarse-grained simulations of lysozyme adsorption.

    PubMed

    Yu, Gaobo; Liu, Jie; Zhou, Jian

    2014-05-01

    Coarse-grained simulations are adopted to study the adsorption behavior of lysozyme on different (hydrophobic, neutral hydrophilic, zwitterionic, negatively charged, and positively charged) surfaces at the mesoscopic microsecond time scale (1.2 μs). Simulation results indicate the following: (i) the conformation change of lysozyme on the hydrophobic surface is bigger than any other studied surfaces; (ii) the active sites of lysozyme are faced to the hydrophobic surface with a "top end-on" orientation, while they are exposed to the liquid phase on the hydrophilic surface with a "back-on" orientation; (iii) the neutral hydrophilic surface can induce the adsorption of lysozyme, while the nonspecific protein adsorption can be resisted by the zwitterionic surface; (iv) when the solution ionic strength is low, lysozyme can anchor on the negatively charged surface easily but cannot adsorb on the positively charged surface; (v) when the solution ionic strength is high, the positively charged lysozyme can also adsorb on the like-charged surface; (vi) the major positive potential center of lysozyme, especially the residue ARG128, plays a vital role in leading the adsorption of lysozyme on charged surfaces; (vii) when the ionic strength is high, a counterion layer is formed above the positively charged surface, which is the key factor why lysozyme can adsorb on a like-charged surface. The coarse-grained method based on the MARTINI force field for proteins and the BMW water model could provide an efficient way to understand protein interfacial adsorption behavior at a greater length scale and time scale.

  20. Self-consistent theory for systems with mesoscopic fluctuations

    NASA Astrophysics Data System (ADS)

    Ciach, A.; Góźdź, W. T.

    2016-10-01

    We have developed a theory for inhomogeneous systems that allows for the incorporation of the effects of mesoscopic fluctuations. A hierarchy of equations relating the correlation and direct correlation functions for the local excess φ ≤ft(\\mathbf{r}\\right) of the volume fraction of particles ζ has been obtained, and an approximation leading to a closed set of equations for the two-point functions has been introduced for the disordered inhomogeneous phase. We have numerically solved the self-consistent equations for one-dimensional (1D) and three-dimensional (3D) models with short-range attraction and long-range repulsion. Predictions for all of the qualitative properties of the 1D model agree with the exact results, but only semi-quantitative agreement is obtained in the simplest version of the theory. The effects of fluctuations in the two 3D models considered are significantly different, despite the very similar properties of these models in the mean-field approximation. In both cases we obtain the sequence of large-small-large compressibility for increasing ζ. The very small compressibility is accompanied by the oscillatory decay of correlations with correlation lengths that are orders of magnitude larger than the size of particles. In one of the two models considered, the small compressibility becomes very small and the large compressibility becomes very large with decreasing temperature, and eventually van der Waals loops appear. Further studies are necessary in order to determine the nature of the strongly inhomogeneous phase present for intermediate volume fractions in 3D.

  1. Mesoscopic dynamics of diffusion-influenced enzyme kinetics.

    PubMed

    Chen, Jiang-Xing; Kapral, Raymond

    2011-01-28

    A particle-based mesoscopic model for enzyme kinetics is constructed and used to investigate the influence of diffusion on the reactive dynamics. Enzymes and enzyme-substrate complexes are modeled as finite-size soft spherical particles, while substrate, product, and solvent molecules are point particles. The system is evolved using a hybrid molecular dynamics-multiparticle collision dynamics scheme. Both the nonreactive and reactive dynamics are constructed to satisfy mass, momentum, and energy conservation laws, and reversible reaction steps satisfy detailed balance. Hydrodynamic interactions among the enzymes and complexes are automatically accounted for in the dynamics. Diffusion manifests itself in various ways, notably in power-law behavior in the evolution of the species concentrations. In accord with earlier investigations, regimes where the product production rate exhibits either monotonic or nonmonotonic behavior as a function of time are found. In addition, the species concentrations display both t(-1/2) and t(-3/2) power-law behavior, depending on the dynamical regime under investigation. For high enzyme volume fractions, cooperative effects influence the enzyme kinetics. The time dependent rate coefficient determined from the mass action rate law is computed and shown to depend on the enzyme concentration. Lifetime distributions of substrate molecules newly released in complex dissociation events are determined and shown to have either a power-law form for rebinding to the same enzyme from which they were released or an exponential form for rebinding to different enzymes. The model can be used and extended to explore a variety of issues related concentration effects and diffusion on enzyme kinetics.

  2. Tunable quasiparticle trapping in Meissner and vortex states of mesoscopic superconductors

    PubMed Central

    Taupin, M.; Khaymovich, I. M.; Meschke, M.; Mel'nikov, A. S.; Pekola, J. P.

    2016-01-01

    Nowadays, superconductors serve in numerous applications, from high-field magnets to ultrasensitive detectors of radiation. Mesoscopic superconducting devices, referring to those with nanoscale dimensions, are in a special position as they are easily driven out of equilibrium under typical operating conditions. The out-of-equilibrium superconductors are characterized by non-equilibrium quasiparticles. These extra excitations can compromise the performance of mesoscopic devices by introducing, for example, leakage currents or decreased coherence time in quantum devices. By applying an external magnetic field, one can conveniently suppress or redistribute the population of excess quasiparticles. In this article, we present an experimental demonstration and a theoretical analysis of such effective control of quasiparticles, resulting in electron cooling both in the Meissner and vortex states of a mesoscopic superconductor. We introduce a theoretical model of quasiparticle dynamics, which is in quantitative agreement with the experimental data. PMID:26980225

  3. Primary thermometry triad at 6 mK in mesoscopic circuits

    NASA Astrophysics Data System (ADS)

    Iftikhar, Z.; Anthore, A.; Jezouin, S.; Parmentier, F. D.; Jin, Y.; Cavanna, A.; Ouerghi, A.; Gennser, U.; Pierre, F.

    2016-09-01

    Quantum physics emerge and develop as temperature is reduced. Although mesoscopic electrical circuits constitute an outstanding platform to explore quantum behaviour, the challenge in cooling the electrons impedes their potential. The strong coupling of such micrometre-scale devices with the measurement lines, combined with the weak coupling to the substrate, makes them extremely difficult to thermalize below 10 mK and imposes in situ thermometers. Here we demonstrate electronic quantum transport at 6 mK in micrometre-scale mesoscopic circuits. The thermometry methods are established by the comparison of three in situ primary thermometers, each involving a different underlying physics. The employed combination of quantum shot noise, quantum back action of a resistive circuit and conductance oscillations of a single-electron transistor covers a remarkably broad spectrum of mesoscopic phenomena. The experiment, performed in vacuum using a standard cryogen-free dilution refrigerator, paves the way towards the sub-millikelvin range with additional thermalization and refrigeration techniques.

  4. Small-angle Scattering Study of Mesoscopic Structures in Charged Gel and Their Evolution in Dehydration

    SciTech Connect

    Sugiyama, M.; Annaka, M.; Hara, K.; Vigild, M. E.; Wignall, George D

    2003-01-01

    Mesoscopic structures, with length scales {approx}10{sup 2} {angstrom}, were investigated by small-angle X-ray and neutron scattering (SAXS and SANS) in several N-isopropylacrylamide-sodium acrylate (NIPA-SA) copolymeric hydrogels with varying [NIPA]/[SA] ratios and water contents. The SAXS experiments reveal that, depending upon the [NIPA]/[SA] ratio, the dehydrated NIPA-SA gel shows two mesoscopic structures: one consists of randomly distributed SA-rich islands in NIPA matrix, while the other is a microphase-separated structure, composed of NIPA-rich and SA-rich domains. In addition, the SANS experiments reveal the mesoscopic structural features during the dehydration process. As the concentration of the network polymers increases, NIPA-rich and water-rich domains segregate in the gel. Then, an electrostatic interaction between the segregated domains induces a microphase-separated structure in the limit of the dehydrated NIPA-SA gel.

  5. Giant Mesoscopic Fluctuations and Long-Range Superconducting Correlations in Superconductor-Ferromagnet Structures

    NASA Astrophysics Data System (ADS)

    Mel'nikov, A. S.; Buzdin, A. I.

    2016-08-01

    The fluctuating superconducting correlations emerging in dirty hybrid structures under the conditions of the strong proximity effect are demonstrated to affect the validity range of the widely used formalism of Usadel equations at mesoscopic scales. In superconductor-ferromagnet structures these giant mesoscopic fluctuations originating from the interference effects for the Cooper pair wave function in the presence of the exchange field can be responsible for an anomalously slow decay of superconducting correlations in a ferromagnet even when the noncollinear and spin-orbit effects are negligible. The resulting sample-to-sample fluctuations of the Josephson current in superconductor-ferromagnetic-superconductor junctions and the local density of states in superconductor-ferromagnetic hybrid structures can provide an explanation of the long-range proximity phenomena observed in mesoscopic samples with collinear magnetization.

  6. Self-organized nanostructures in surface chemical reactions: Mechanisms and mesoscopic modeling

    NASA Astrophysics Data System (ADS)

    Hildebrand, M.

    2002-03-01

    Nanoscale patterns can form in reactive adsorbates on catalytic surfaces as a result of attractive lateral interactions. These structures can be described within a mesoscopic theory that is derived by coarse graining the microscopic master equation thus providing a link between microscopic lattice models and reaction-diffusion equations. Such mesoscopic models allow to systematically investigate mechanisms responsible for the formation of nanoscale nonequilibrium patterns in reactive condensed matter. We have found that stationary and traveling nanostructures may result from the interplay of the attractive lateral interactions and nonequilibrium reactions. Besides reviewing these results, a detailed investigation of a single reactive adsorbate in the presence of attractive lateral interactions and global coupling through the gas phase is presented. Finally, it is outlined how a mesoscopic theory should be constructed for a particular scanning tunneling microscopy experiment [the oxidation of hydrogen on a Pt(111) surface] in order to overcome the failure of a corresponding reaction-diffusion model to quantitatively reproduce the experiments.

  7. Space experiment "Cellular Responses to Radiation in Space (CellRad)": Hardware and biological system tests.

    PubMed

    Hellweg, Christine E; Dilruba, Shahana; Adrian, Astrid; Feles, Sebastian; Schmitz, Claudia; Berger, Thomas; Przybyla, Bartos; Briganti, Luca; Franz, Markus; Segerer, Jürgen; Spitta, Luis F; Henschenmacher, Bernd; Konda, Bikash; Diegeler, Sebastian; Baumstark-Khan, Christa; Panitz, Corinna; Reitz, Günther

    2015-11-01

    One factor contributing to the high uncertainty in radiation risk assessment for long-term space missions is the insufficient knowledge about possible interactions of radiation with other spaceflight environmental factors. Such factors, e.g. microgravity, have to be considered as possibly additive or even synergistic factors in cancerogenesis. Regarding the effects of microgravity on signal transduction, it cannot be excluded that microgravity alters the cellular response to cosmic radiation, which comprises a complex network of signaling pathways. The purpose of the experiment "Cellular Responses to Radiation in Space" (CellRad, formerly CERASP) is to study the effects of combined exposure to microgravity, radiation and general space flight conditions on mammalian cells, in particular Human Embryonic Kidney (HEK) cells that are stably transfected with different plasmids allowing monitoring of proliferation and the Nuclear Factor κB (NF-κB) pathway by means of fluorescent proteins. The cells will be seeded on ground in multiwell plate units (MPUs), transported to the ISS, and irradiated by an artificial radiation source after an adaptation period at 0 × g and 1 × g. After different incubation periods, the cells will be fixed by pumping a formaldehyde solution into the MPUs. Ground control samples will be treated in the same way. For implementation of CellRad in the Biolab on the International Space Station (ISS), tests of the hardware and the biological systems were performed. The sequence of different steps in MPU fabrication (cutting, drilling, cleaning, growth surface coating, and sterilization) was optimized in order to reach full biocompatibility. Different coatings of the foil used as growth surface revealed that coating with 0.1 mg/ml poly-D-lysine supports cell attachment better than collagen type I. The tests of prototype hardware (Science Model) proved its full functionality for automated medium change, irradiation and fixation of cells. Exposure of

  8. Space experiment "Cellular Responses to Radiation in Space (CELLRAD)": Hardware and biological system tests

    NASA Astrophysics Data System (ADS)

    Hellweg, Christine E.; Dilruba, Shahana; Adrian, Astrid; Feles, Sebastian; Schmitz, Claudia; Berger, Thomas; Przybyla, Bartos; Briganti, Luca; Franz, Markus; Segerer, Jürgen; Spitta, Luis F.; Henschenmacher, Bernd; Konda, Bikash; Diegeler, Sebastian; Baumstark-Khan, Christa; Panitz, Corinna; Reitz, Günther

    2015-11-01

    One factor contributing to the high uncertainty in radiation risk assessment for long-term space missions is the insufficient knowledge about possible interactions of radiation with other spaceflight environmental factors. Such factors, e.g. microgravity, have to be considered as possibly additive or even synergistic factors in cancerogenesis. Regarding the effects of microgravity on signal transduction, it cannot be excluded that microgravity alters the cellular response to cosmic radiation, which comprises a complex network of signaling pathways. The purpose of the experiment ;Cellular Responses to Radiation in Space; (CELLRAD, formerly CERASP) is to study the effects of combined exposure to microgravity, radiation and general space flight conditions on mammalian cells, in particular Human Embryonic Kidney (HEK) cells that are stably transfected with different plasmids allowing monitoring of proliferation and the Nuclear Factor κB (NF-κB) pathway by means of fluorescent proteins. The cells will be seeded on ground in multiwell plate units (MPUs), transported to the ISS, and irradiated by an artificial radiation source after an adaptation period at 0 × g and 1 × g. After different incubation periods, the cells will be fixed by pumping a formaldehyde solution into the MPUs. Ground control samples will be treated in the same way. For implementation of CELLRAD in the Biolab on the International Space Station (ISS), tests of the hardware and the biological systems were performed. The sequence of different steps in MPU fabrication (cutting, drilling, cleaning, growth surface coating, and sterilization) was optimized in order to reach full biocompatibility. Different coatings of the foil used as growth surface revealed that coating with 0.1 mg/ml poly-D-lysine supports cell attachment better than collagen type I. The tests of prototype hardware (Science Model) proved its full functionality for automated medium change, irradiation and fixation of cells. Exposure of

  9. A Test of the Relationship between Reading Ability & Standardized Biology Assessment Scores

    ERIC Educational Resources Information Center

    Allen, Denise A.

    2014-01-01

    Little empirical evidence suggested that independent reading abilities of students enrolled in biology predicted their performance on the Biology I Graduation End-of-Course Assessment (ECA). An archival study was conducted at one Indiana urban public high school in Indianapolis, Indiana, by examining existing educational assessment data to test…

  10. A Test of the Relationship between Reading Ability & Standardized Biology Assessment Scores

    ERIC Educational Resources Information Center

    Allen, Denise A.

    2014-01-01

    Little empirical evidence suggested that independent reading abilities of students enrolled in biology predicted their performance on the Biology I Graduation End-of-Course Assessment (ECA). An archival study was conducted at one Indiana urban public high school in Indianapolis, Indiana, by examining existing educational assessment data to test…

  11. Selected Biology Behavioral Objectives and Test Items for Grades 4-6.

    ERIC Educational Resources Information Center

    Leithwood, Kenneth A.

    This booklet, compiled by the Ontario Institute for Studies in Education, lists behavioral objectives for biology in grades 4-6. The major areas of biology objectives presented are relations among plants, animals, and the environment; identifying and classifying plants and animals; and structures and functions of plants and animals. Each major…

  12. Sagnac rotational phase shifts in a mesoscopic electron interferometer with spin-orbit interactions

    SciTech Connect

    Zivkovic, Marko; Jaeaeskelaeinen, Markku; Search, Christopher P.; Djuric, Ivana

    2008-03-15

    The Sagnac effect is an important phase coherent effect in optical and atom interferometers where rotations of the interferometer with respect to an inertial reference frame result in a shift in the interference pattern proportional to the rotation rate. Here, we analyze the Sagnac effect in a mesoscopic semiconductor electron interferometer. We include in our analysis the Rashba spin-orbit interactions in the ring. Our results indicate that spin-orbit interactions increase the rotation-induced phase shift. We discuss the potential experimental observability of the Sagnac phase shift in such mesoscopic systems.

  13. Efficient Compact-Layer-Free, Hole-Conductor-Free, Fully Printable Mesoscopic Perovskite Solar Cell.

    PubMed

    Jiang, Xixi; Xiong, Yuli; Mei, Anyi; Rong, Yaoguang; Hu, Yue; Hong, Li; Jin, Yingxia; Liu, Qingju; Han, Hongwei

    2016-10-05

    A compact-layer-free, hole-conductor-free, fully printable mesoscopic perovskite solar cell presents a power conversion efficiency of over 13%, which is comparable to that of the device with a TiO2 compact layer. The different wettability of the perovskite precursor solution on the surface of FTO and TiO2 possesses a significant effect on realizing efficient mesoscopic perovskite solar cell. This result shows a promising future in printable solar cells by further simplifying the fabrication process and lowering the preparation costs.

  14. Decoherence as attenuation of mesoscopic echoes in a spin-chain channel

    SciTech Connect

    Alvarez, Gonzalo A.; Danieli, Ernesto P.; Levstein, Patricia R.; Pastawski, Horacio M.

    2010-07-15

    An initial local excitation in a confined quantum system evolves, exploring the whole system and returning to the initial position as a mesoscopic echo at the Heisenberg time. We consider two weakly coupled spin chains, a spin ladder, where one is a quantum channel while the other represents an environment. We quantify decoherence in the quantum channel through the attenuation of the mesoscopic echoes. We evaluate decoherence rates for different ratios between sources of amplitude fluctuation and dephasing in the interchain interaction Hamiltonian. The many-body dynamics is seen as a one-body evolution with a decoherence rate given by the Fermi golden rule.

  15. Inferring local competition intensity from patch size distributions: a test using biological soil crusts

    USGS Publications Warehouse

    Bowker, Matthew A.; Maestre, Fernando T.

    2012-01-01

    Dryland vegetation is inherently patchy. This patchiness goes on to impact ecology, hydrology, and biogeochemistry. Recently, researchers have proposed that dryland vegetation patch sizes follow a power law which is due to local plant facilitation. It is unknown what patch size distribution prevails when competition predominates over facilitation, or if such a pattern could be used to detect competition. We investigated this question in an alternative vegetation type, mosses and lichens of biological soil crusts, which exhibit a smaller scale patch-interpatch configuration. This micro-vegetation is characterized by competition for space. We proposed that multiplicative effects of genetics, environment and competition should result in a log-normal patch size distribution. When testing the prevalence of log-normal versus power law patch size distributions, we found that the log-normal was the better distribution in 53% of cases and a reasonable fit in 83%. In contrast, the power law was better in 39% of cases, and in 8% of instances both distributions fit equally well. We further hypothesized that the log-normal distribution parameters would be predictably influenced by competition strength. There was qualitative agreement between one of the distribution's parameters (μ) and a novel intransitive (lacking a 'best' competitor) competition index, suggesting that as intransitivity increases, patch sizes decrease. The correlation of μ with other competition indicators based on spatial segregation of species (the C-score) depended on aridity. In less arid sites, μ was negatively correlated with the C-score (suggesting smaller patches under stronger competition), while positive correlations (suggesting larger patches under stronger competition) were observed at more arid sites. We propose that this is due to an increasing prevalence of competition transitivity as aridity increases. These findings broaden the emerging theory surrounding dryland patch size distributions

  16. Science Library of Test Items. Volume Seventeen. A Collection of Multiple Choice Test Items Relating Mainly to Biology.

    ERIC Educational Resources Information Center

    New South Wales Dept. of Education, Sydney (Australia).

    As one in a series of test item collections developed by the Assessment and Evaluation Unit of the Directorate of Studies, items are made available to teachers for the construction of unit tests or term examinations or as a basis for class discussion. Each collection was reviewed for content validity and reliability. The test items meet syllabus…

  17. Dynamic studies of proton diffusion in mesoscopic heterogeneous matrix

    PubMed Central

    Gutman, M.; Nachliel, E.; Kiryati, S.

    1992-01-01

    The thin water layer, as found in chloroplast or mitochondria, is confined between low dielectric amphypathic surfaces a few nm apart. The physical properties of this mesoscopic space, and how its dimensions affect the rate of chemical reactions proceeding in it, is the subject for this study. The method selected for this purpose is time resolved fluorometry which can monitor the reversible dissociation of a proton from excited molecule of pyranine (8 hydroxy pyrene 1,3,6 tri sulfonate) trapped in thin water layers of a multilamellar vesicle made of neutral or slightly charged phospholipids. The results were analyzed by a computer program of N. Agmon (Pines, E., D. Huppert, and N. Agmon. 1988. J. Am. Chem. Soc. 88:5620-5630) that simulates the diffusion of a proton, subjected to electrostatic attraction, in a thin water layer enclosed between low affinity, proton binding surfaces. The analysis determines the diffusion coefficient of the proton, the effective dielectric constant of the water and the water accessibility of the phosphomoieties of the lipids. These parameters were measured for various lipids [egg-phosphatidylcholine (egg PC), dipalmitoyl phosphatidylcholine (DPPC), cholesterol + DPPC (1:1) and egg PC plus phosphatidyl serine (9:1)] and under varying osmotic pressure which reduces the width of the water layer down to ∼10 ∼ across. We found that: (a) The effective dielectric constant of the aqueous layer, depending on the lipid composition, is ∼40. (b) The diffusion coefficient of the proton in the thin layer (30-10 ∼ across) is that measured in bulk water D = 9.3 10-5 cm2/s, indicating that the water retains its normal liquid state even on contact with the membrane. (c) The reactivity of the phosphomoiety, quantitated by rate of its reaction with proton, diminishes under lateral pressure which reduces the surface area per lipid. We find no evidence for abnormal dynamics of proton transfer at the lipid water interface which, by any mechanism

  18. Energy utilization in fluctuating biological energy converters.

    PubMed

    Szőke, Abraham; Hajdu, Janos

    2016-05-01

    We have argued previously [Szoke et al., FEBS Lett. 553, 18-20 (2003); Curr. Chem. Biol. 1, 53-57 (2007)] that energy utilization and evolution are emergent properties based on a small number of established laws of physics and chemistry. The relevant laws constitute a framework for biology on a level intermediate between quantum chemistry and cell biology. There are legitimate questions whether these concepts are valid at the mesoscopic level. Such systems fluctuate appreciably, so it is not clear what their efficiency is. Advances in fluctuation theorems allow the description of such systems on a molecular level. We attempt to clarify this topic and bridge the biochemical and physical descriptions of mesoscopic systems.

  19. Energy utilization in fluctuating biological energy converters

    PubMed Central

    Szőke, Abraham; Hajdu, Janos

    2016-01-01

    We have argued previously [Szoke et al., FEBS Lett. 553, 18–20 (2003); Curr. Chem. Biol. 1, 53–57 (2007)] that energy utilization and evolution are emergent properties based on a small number of established laws of physics and chemistry. The relevant laws constitute a framework for biology on a level intermediate between quantum chemistry and cell biology. There are legitimate questions whether these concepts are valid at the mesoscopic level. Such systems fluctuate appreciably, so it is not clear what their efficiency is. Advances in fluctuation theorems allow the description of such systems on a molecular level. We attempt to clarify this topic and bridge the biochemical and physical descriptions of mesoscopic systems. PMID:27191009

  20. Mesoscopic Strains Maps in Woven Composite Laminas During Off-axis Tension

    NASA Astrophysics Data System (ADS)

    Anzelotti, G.; Nicoletto, G.; Riva, E.

    2010-06-01

    The mechanics of woven carbon-fiber reinforced plastic (CFRP) composites is influenced by the complex architecture of the reinforcement phase. Computational (i.e. finite element based) approaches have been used increasingly to model not only the global laminate stiffness, but also damage evolution and laminate strength. The modeling combines the identification of the architectural unit cell (UC), the selection of suitable constitutive models of the different phases, the creation of a fine discretization of the UC in finite elements, the application of an incremental solution procedure that solves iteratively for the stresses and strains in the UC, [1]. The experimental validation of computational models is carried out mainly at the macroscopical level, i.e. simulation of the macroscopic stress-strain curve. Damage, however, is a localized, straindependent phenomenon and therefore only accurate strain distribution within the UC (at the mesolevel) can identify critical conditions in terms of damage location, extension and evolution. The validation of computational damage procedures is a key task and full-field optical strain analysis methods appear the ideal instrument. However, only limited examples of direct finte element method (FEM) vs experimental strain correlation are found because of the limited sensitivity and spatial resolution of some techniques and the complexity and applicative difficulty of others. The aim of the present paper is to present the application of the digital image correlation (DIC) technique, [2], to the full-field strain analysis at the mesoscopic level (i.e. within the UC) of a woven CFRP lamina when the direction of loading forms an angle to the material direction. The material under consideration is a woven carbon fiber reinforced epoxy composite. Orthogonal yarns, each made of of several thousand fibers, are woven according the twill-weave architecture is shown in Fig. 1a. Single-ply laminas were manufactured and tested to eliminate

  1. Comparative study of biological activity of insulins of lower vertebrates in the novel adenylyl cyclase test-system.

    PubMed

    Kuznetsova, L; Shpakov, A; Rusakov, Yu; Plesneva, S; Bondareva, V; Pertseva, M

    2003-11-15

    The biological activity of insulins of lower vertebrates (teleosts-Oncorhynchus gorbuscha, Scorpaena porcus, chondrosteans-Acipenser guldenstaedti and cyclostomates-Lamperta fluviatilis) was studied and compared with that of standard pig insulin. The determination of biological activity was made using the novel adenylyl cyclase (AC) test-system based on the adenylyl cyclase signaling mechanism (ACSM) of insulin action discovered earlier by the authors. The biological activity of insulins was estimated as EC(50), i.e. concentration leading to half-maximal activating effect of the hormone (10(-11)-10(-7) M), in vitro, on adenylyl cyclase in two types of the target tissues: in membrane fractions of the muscles of rat and mollusc Anodonta cygnea. In rat, the efficiency of insulins was found to decrease in the following order: pig insulin>scorpaena insulin>gorbuscha insulin>sturgeon insulin>lamprey insulin. In the mollusc, the order was different: sturgeon insulin>scorpaena insulin>pig insulin>gorbuscha insulin. Lamprey insulin at the same concentrations did not apparently reach the maximal adenylyl cyclase activating effect. The suggestion was made that differences in the biological activity of insulins depend on the hormone structure and a number of indexes characteristic of the adenylyl cyclase test-system in the vertebrate and invertebrate tissues. The proposed adenylyl cyclase test-system is highly sensitive to insulin at physiological concentrations, has good reproduction and is easy to apply.

  2. Introscopy in nano- and mesoscopic physics: Single electronics and quantum ballistics

    NASA Astrophysics Data System (ADS)

    Tkachenko, V. A.; Tkachenko, O. A.; Kvon, Z. D.; Latyshev, A. V.; Aseev, A. L.

    2016-09-01

    A method is presented to be used in a computational experiment aimed at studying the internal structure of nano- and mesoscopic objects, i.e., conducting subsystems and quantum phenomena in solid submicron objects, which demonstrate an individual behavior of low-temperature resistance.

  3. Conceptual density functional theory for electron transfer and transport in mesoscopic systems.

    PubMed

    Bueno, Paulo R; Miranda, David A

    2017-02-22

    Molecular and supramolecular systems are essentially mesoscopic in character. The electron self-exchange, in the case of energy fluctuations, or electron transfer/transport, in the case of the presence of an externally driven electrochemical potential, between mesoscopic sites is energetically driven in such a manner where the electrochemical capacitance (C[small mu, Greek, macron]) is fundamental. Thus, the electron transfer/transport through channels connecting two distinct energetic (ΔE[small mu, Greek, macron]) and spatially separated mesoscopic sites is capacitively modulated. Remarkably, the relationship between the quantum conductance (G) and the standard electrochemical rate constant (kr), which is indispensable to understanding the physical and chemical characteristics governing electron exchange in molecular scale systems, was revealed to be related to C[small mu, Greek, macron], that is, C[small mu, Greek, macron] = G/kr. Accordingly, C[small mu, Greek, macron] is the proportional missing term that controls the electron transfer/transport in mesoscopic systems in a wide-range, and equally it can be understood from first principles density functional quantum mechanical approaches. Indeed the differences in energy between states is calculated (or experimentally accessed) throughout the electrochemical capacitance as ΔE[small mu, Greek, macron] = β/C[small mu, Greek, macron], and thus constitutes the driving force for G and/or kr, where β is only a proportional constant that includes the square of the unit electron charge times the square of the number of electron particles interchanged.

  4. Random-matrix-theory approach to mesoscopic fluctuations of heat current.

    PubMed

    Schmidt, Martin; Kottos, Tsampikos; Shapiro, Boris

    2013-08-01

    We consider an ensemble of fully connected networks of N oscillators coupled harmonically with random springs and show, using random-matrix-theory considerations, that both the average phonon heat current and its variance are scale invariant and take universal values in the large N limit. These anomalous mesoscopic fluctuations is the hallmark of strong correlations between normal modes.

  5. Random-matrix-theory approach to mesoscopic fluctuations of heat current

    NASA Astrophysics Data System (ADS)

    Schmidt, Martin; Kottos, Tsampikos; Shapiro, Boris

    2013-08-01

    We consider an ensemble of fully connected networks of N oscillators coupled harmonically with random springs and show, using random-matrix-theory considerations, that both the average phonon heat current and its variance are scale invariant and take universal values in the large N limit. These anomalous mesoscopic fluctuations is the hallmark of strong correlations between normal modes.

  6. Linear and nonlinear mesoscopic thermoelectric transport with coupling with heat baths

    NASA Astrophysics Data System (ADS)

    Jiang, Jian-Hua; Imry, Yoseph

    2016-12-01

    Decades of research on thermoelectrics stimulated by the fact that nano- and meso-scale thermoelectric transport could yield higher energy conversion efficiency and output power has recently uncovered a new direction on inelastic thermoelectric effects. We introduce the history, motivation, and perspectives on mesoscopic inelastic thermoelectric effects. xml:lang="fr"

  7. Mesoscopic helical architectures via self-assembly of porphyrin-based discotic systems.

    PubMed

    Vela, Sonia; Berrocal, José Augusto; Atienza, Carmen; Meijer, E W; Martín, Nazario

    2017-04-06

    Mesoscopic super-helices with preferred helicity have been serendipitously formed from the self-assembly of electroactive extended core discotic molecules. The investigation at dilute concentrations reveals intramolecular hydrogen-bonding and π-π stacking interactions as the driving force of the chiral self-assembly at different length scales.

  8. Reflective mesoscopic spectroscopy for noninvasive detection of reflective index alternations at nano-scale

    NASA Astrophysics Data System (ADS)

    Tao, Yuanhao; Ding, Zhihua

    2011-01-01

    Cancer has been one of the most serious threats to human life. However, there is no substantial improvement in overall treatment of cancer patients. One of the key reasons is the unavailability of convenient method to detect cellular alterations in ultra-early stage of carcinogenesis processes, where genetic aberrations at nano-scale have not yet resulted in histological changes. In this paper, we described an optical method based on reflective mesoscopic spectroscopy for ultra-early cancer detection. According to mesoscopic light transport theory, photons propagating in one dimension (1D) within a weakly disordered medium have the non-self-averaging effect. Reflected signal after 1D propagating is sensitive to any length scale of refractive index fluctuations due to multiple interferences of light waves travelling along 1D trajectory. The principle of mesoscopic spectroscopy for perceiving reflective index fluctuations at length scale of nanometers is introduced. A system for the measurement of reflective mesoscopic spectroscopy based on spatial-incoherence broadband source and spectrometer is established. Simulations on light propagation in cell-emulating model with controlled refractive index distribution are done by finite-difference time-domain (FDTD) approach.

  9. A framework towards understanding mesoscopic phenomena: Emergent unpredictability, symmetry breaking and dynamics across scales

    NASA Astrophysics Data System (ADS)

    Qian, Hong; Ao, Ping; Tu, Yuhai; Wang, Jin

    2016-11-01

    By integrating four lines of thoughts: symmetry breaking originally advanced by Anderson, bifurcation from nonlinear dynamical systems, Landau's phenomenological theory of phase transition, and the mechanism of emergent rare events first studied by Kramers, we introduce a possible framework for understanding mesoscopic dynamics that links (i) fast microscopic (lower level) motions, (ii) movements within each basin-of-attraction at the mid-level, and (iii) higher-level rare transitions between neighboring basins, which have slow rates that decrease exponentially with the size of the system. In this mesoscopic framework, the fast dynamics is represented by a rapidly varying stochastic process and the mid-level by a nonlinear dynamics. Multiple attractors arise as emergent properties of the nonlinear systems. The interplay between the stochastic element and nonlinearity, the essence of Kramers' theory, leads to successive jump-like transitions among different basins. We argue each transition is a dynamic symmetry breaking, with the potential of exhibiting Thom-Zeeman catastrophe as well as phase transition with the breakdown of ergodicity (e.g., cell differentiation). The slow-time dynamics of the nonlinear mesoscopic system is not deterministic, rather it is a discrete stochastic jump process. The existence of these discrete states and the Markov transitions among them are both emergent phenomena. This emergent stochastic jump dynamics then serves as the stochastic element for the nonlinear dynamics of a higher level aggregates on an even larger spatial and slower time scales (e.g., evolution). This description captures the hierarchical structure outlined by Anderson and illustrates two distinct types of limit of a mesoscopic dynamics: A long-time ensemble thermodynamics in terms of time t → ∞ followed by the size of the system N → ∞ , and a short-time trajectory steady state with N → ∞ followed by t → ∞ . With these limits, symmetry breaking and cusp

  10. A material combination principle for highly efficient polymer solar cells investigated by mesoscopic phase heterogeneity.

    PubMed

    Yan, Han; Li, Denghua; He, Chang; Wei, Zhixiang; Yang, Yanlian; Li, Yongfang

    2013-12-07

    Organic solar cells have become a promising energy conversion candidate because of their unique advantages. Novel fullerene derivatives, as a common acceptor, can increase power conversion efficiency (PCE) by increasing the open-circuit voltage. As a representative acceptor, Indene-C60 bisadduct (ICBA) can reach high efficiency with poly(3-hexylthiophene) (P3HT). On the other hand, the novel synthesized polymers mainly aimed to broaden the optical absorption range have steadily promoted efficiency to higher than 9%. However, it is challenging to obtain the desired result by simply combining ICBA with other high-efficiency donors. Thus, P3HT or a high-efficiency polymer PBDTTT-C-T (copolymer of thienyl-substituted BDT with substituted TT) is used as donor and PCBM or ICBA as acceptor in this article to clarify the mechanism behind these materials. The optical and photovoltaic properties of the materials are studied for pair-wise combination. Among these four material groups, the highest PCE of 6.2% is obtained for the PBDTTT-C-T/PCBM combination while the lowest PCE of 3.5% is obtained for the PBDTTT-C-T/ICBA combination. The impact of the mesoscopic heterogeneity on the local mesoscopic photoelectric properties is identified by photo-conductive AFM (pc-AFM), and the consistence between the mesoscopic properties and the macroscopic device performances is also observed. Based on these results, an interface combined model is proposed based on the mesoscopic phase heterogeneity. This study provides a new view on the rational selection of photovoltaic materials, where, aside from the traditional energy level and absorption spectrum matching, the matching of mesoscopic heterogeneity must also be considered.

  11. Critical tests for determination of microbiological quality and biological activity in commercial vermicompost samples of different origins.

    PubMed

    Grantina-Ievina, Lelde; Andersone, Una; Berkolde-Pīre, Dace; Nikolajeva, Vizma; Ievinsh, Gederts

    2013-12-01

    The aim of the present paper was to show that differences in biological activity among commercially produced vermicompost samples can be found by using a relatively simple test system consisting of microorganism tests on six microbiological media and soilless seedling growth tests with four vegetable crop species. Significant differences in biological properties among analyzed samples were evident both at the level of microbial load as well as plant growth-affecting activity. These differences were mostly manufacturer- and feedstock-associated, but also resulted from storage conditions of vermicompost samples. A mature vermicompost sample that was produced from sewage sludge still contained considerable number of Escherichia coli. Samples from all producers contained several potentially pathogenic fungal species such as Aspergillus fumigatus, Pseudallescheria boidii, Pseudallescheria fimeti, Pseudallescheria minutispora, Scedosporium apiospermum, Scedosporium prolificans, Scopulariopsis brevicaulis, Stachybotrys chartarum, Geotrichum spp., Aphanoascus terreus, and Doratomyces columnaris. In addition, samples from all producers contained plant growth-promoting fungi from the genera Trichoderma and Mortierella. The described system can be useful both for functional studies aiming at understanding of factors affecting quality characteristics of vermicompost preparations and for routine testing of microbiological quality and biological activity of organic waste-derived composts and vermicomposts.

  12. Testing biological effects of hand-washing grey water for reuse in irrigation on an urban farm: a case study.

    PubMed

    Khan, Mohammad Zain; Sim, Yei Lin; Lin, Yang Jian; Lai, Ka Man

    2013-01-01

    The feasibility of reusing hand-washing grey water contaminated with antibacterial hand-washing liquid for irrigation purposes in an urban farm is explored in this case study. Experiments are carried out to investigate if the quality of this grey water allows for its reuse in agriculture as per the guidelines established by the World Health Organization (WHO). However, there is no guideline to test the biological effect of grey water prior to agricultural use. It is plausible that the antibacterial property of the grey water can harm the soil microbial system and plants when applied to land, even if all other water quality parameters satisfy the WHO limit. We use algae (Chlorella vulgaris) and indigenous soil bacteria as initial plant and soil bacteria indicators, respectively, to test the potential inhibition of the water on plants and soil bacteria. Results show that the chemical oxygen demand (COD) of the grey water is 10% higher than the WHO permissible level, while all other water quality parameters are within the limits after four days of our experimental period. An inhibitory effect is observed in all of the biological tests. However, the inhibitory effect on algae and soil bacteria is not observed after the four-day period. The case study demonstrates a new approach for testing the biological effect of grey water, which can be used in conjunction with the WHO guideline, and provides data for this urban farm to set up a future water treatment system for grey-water reuse in irrigation.

  13. Measuring the Outcome of At-Risk Students on Biology Standardized Tests When Using Different Instructional Strategies

    NASA Astrophysics Data System (ADS)

    Burns, Dana

    Over the last two decades, online education has become a popular concept in universities as well as K-12 education. This generation of students has grown up using technology and has shown interest in incorporating technology into their learning. The idea of using technology in the classroom to enhance student learning and create higher achievement has become necessary for administrators, teachers, and policymakers. Although online education is a popular topic, there has been minimal research on the effectiveness of online and blended learning strategies compared to the student learning in a traditional K-12 classroom setting. The purpose of this study was to investigate differences in standardized test scores from the Biology End of Course exam when at-risk students completed the course using three different educational models: online format, blended learning, and traditional face-to-face learning. Data was collected from over 1,000 students over a five year time period. Correlation analyzed data from standardized tests scores of eighth grade students was used to define students as "at-risk" for failing high school courses. The results indicated a high correlation between eighth grade standardized test scores and Biology End of Course exam scores. These students were deemed "at-risk" for failing high school courses. Standardized test scores were measured for the at-risk students when those students completed Biology in the different models of learning. Results indicated significant differences existed among the learning models. Students had the highest test scores when completing Biology in the traditional face-to-face model. Further evaluation of subgroup populations indicated statistical differences in learning models for African-American populations, female students, and for male students.

  14. Directed self-assembly of mesoscopic components for led applications

    NASA Astrophysics Data System (ADS)

    Tkachenko, Anton

    Light-emitting diodes (LEDs) constitute a rapidly evolving and fast growing technology that promises to replace incandescent bulbs and compact fluorescent lights in many illumination applications. Large-area LED luminaires have a capability to transform lighting by providing a venue for development of smart lighting systems with additional benefits, such as visible light communications, sensing, health and productivity improvement through color temperature control, capability of creating "virtual sky" ceiling, and many others. The objective of this work is to explore directed self-assembly (DSA) approaches suitable for cost-effective assembly of large amount of LEDs and other mesoscopic (i.e. millimeter and sub-millimeter) electronic components and thus to enable manufacturing of smart lighting luminaires. Existing alternative approaches for assembly of semiconductor dies are examined including transfer printing, laser-assisted die transfer, and various directed self-assembly approaches using shape-recognition, magnetic and capillary forces, etc. After comparing their advantages and limitations, we developed two approaches to magnetic force-assisted DSA of LEDs on a large-area substrate in liquid and air medium. The first approach involves pick-up of buoyant and magnetic dies from the liquid surface onto the flexible substrate in a roll-to-roll process. The possibility of high-speed assembly of LED dies is demonstrated, but with a low yield due to the influence of the capillary force of the carrier liquid and the difficulty in ensuring reliable supply of dies to the assembly interface. To overcome the aforementioned challenges this process was modified to assemble the dies by sinking them onto the receiving substrate with a stencil mask on top, demonstrating LED assembly with a very low error rate but at a lower speed. A solder-assisted self-alignment is used to further improve placement precision and to ensure the proper orientation of the dies. The second

  15. The effects of co-teaching on student test performance and attitudes towards science in high school biology

    NASA Astrophysics Data System (ADS)

    Cole, Virginia Scott

    Reform efforts in response to the inclusion of students with disabilities into general education classrooms have become necessary to shift students' placements into the science classroom. An investigation into the effects of co-teaching in high school biology classrooms was conducted to explore the impact of two models of co-teaching on biology students' achievement and their attitudes towards science. Quantitative data were collected using a diagnostic exam, student chapter test scores, and the Scientific Attitude Inventory II (SAI II) (Moore & Foy, 1997). Additionally, qualitative data were collected from student and teacher interviews, as well as reflections recorded by the general education participating teacher. The study occurred at a predominantly African-American high school in an Alabama city school with approximately 700 students. The population for the study was composed of 62 high school biology students, with 18 of those students placed inclusively in the biology classroom as a result of No Child Left Behind legislation. The participating teachers consisted of one general education biology teacher and one highly qualified, science special education teacher. Twelve students, along with the special education participating teacher, were interviewed and provided qualitative data after completion of the study. The general education teacher provided teacher reflection responses to contribute qualitatively on the impact of co-teaching in high school biology. Quantitative data analysis was performed using descriptive statistics, ANOVA, and paired samples t tests analyses. ANOVA results revealed that there were no changes in student test scores of achievement due to the models of instruction implemented. The implementation of no co-teaching, station teaching, and the one-teaching, one-drifting co-teaching models of instruction did not result in significant changes in students' achievement. Furthermore, paired samples t tests revealed no change in students

  16. Determination of ichthiomycin concentration by biological test with Cyprinus carpio L.

    PubMed

    Gameyska, Y; Popov, K; Ognianov, I; Tishinova, R; Rachev, R

    1993-01-01

    We have found out that one-year-old carps are extremely sensitive to ichthiomycin in concentrations between 25-125 micrograms/dm3. This fact permitted the use of biological methods for determination of ichthiomycin concentrations in cultural medium of Streptomyces levoris 1107 or crude preparations of the antibiotic.

  17. Membrane materials for storing biological samples intended for comparative nanotoxicological testing

    NASA Astrophysics Data System (ADS)

    Metelkin, A.; Kuznetsov, D.; Kolesnikov, E.; Chuprunov, K.; Kondakov, S.; Osipov, A.; Samsonova, J.

    2015-11-01

    The study is aimed at identifying the samples of most promising membrane materials for storing dry specimens of biological fluids (Dried Blood Spots, DBS technology). Existing sampling systems using cellulose fiber filter paper have a number of drawbacks such as uneven distribution of the sample spot, dependence of the spot spreading area on the individual biosample properties, incomplete washing-off of the sample due to partially inconvertible sorption of blood components on cellulose fibers, etc. Samples of membrane materials based on cellulose, polymers and glass fiber with applied biosamples were studied using methods of scanning electron microscopy, FT-IR spectroscopy and surface-wetting measurement. It was discovered that cellulose-based membrane materials sorb components of biological fluids inside their structure, while membranes based on glass fiber display almost no interaction with the samples and biological fluid components dry to films in the membrane pores between the structural fibers. This characteristic, together with the fact that membrane materials based on glass fiber possess sufficient strength, high wetting properties and good storage capacity, attests them as promising material for dry samples of biological fluids storage systems.

  18. The Relationship of Programmed Instruction to Test and Discussion Performance among Beginning College Biology Students.

    ERIC Educational Resources Information Center

    Parker, Gary Eugene

    The objective of this research was to contrast the effects of two instructional techniques (programmed vs. conventional) used in beginning college biology courses. The experimental technique involved the use of programmed textbook units within the typical course syllabus. Ninety students were involved in the study. Four programmed texts were used.…

  19. Testing Effect and Complex Comprehension in a Large Introductory Undergraduate Biology Course

    ERIC Educational Resources Information Center

    Pagliarulo, Christopher L.

    2011-01-01

    Traditional undergraduate biology courses are content intensive, requiring students to understand and remember large amounts of information in short periods of time. Yet most students maintain little of the material encountered during their education. Poor knowledge retention is a main cause of academic failure and high undergraduate attrition…

  20. Testing Effect and Complex Comprehension in a Large Introductory Undergraduate Biology Course

    ERIC Educational Resources Information Center

    Pagliarulo, Christopher L.

    2011-01-01

    Traditional undergraduate biology courses are content intensive, requiring students to understand and remember large amounts of information in short periods of time. Yet most students maintain little of the material encountered during their education. Poor knowledge retention is a main cause of academic failure and high undergraduate attrition…

  1. The performances of the chi-square test and complexity measures for signal recognition in biological sequences.

    PubMed

    Pirhaji, Leila; Kargar, Mehdi; Sheari, Armita; Poormohammadi, Hadi; Sadeghi, Mehdi; Pezeshk, Hamid; Eslahchi, Changiz

    2008-03-21

    With large amounts of experimental data, modern molecular biology needs appropriate methods to deal with biological sequences. In this work, we apply a statistical method (Pearson's chi-square test) to recognize the signals appear in the whole genome of the Escherichia coli. To show the effectiveness of the method, we compare the Pearson's chi-square test with linguistic complexity on the complete genome of E. coli. The results suggest that Pearson's chi-square test is an efficient method for distinguishing genes (coding regions) form pseudogenes (noncoding regions). On the other hand, the performance of the linguistic complexity is much lower than the chi-square test method. We also use the Pearson's chi-square test method to determine which parts of the Open Reading Frame (ORF) have significant effect on discriminating genes form pseudogenes. Moreover, different complexity measures and Pearson's chi-square test applied on the genes with high value of Pearson's chi-square statistic. We also compute the measures on homologous of these genes. The results illustrate that there is a region near the start codon with high value of chi-square statistic and low complexity that is conserve between homologous genes.

  2. Cosmic radiation exposure of biological test systems during the EXPOSE-E mission.

    PubMed

    Berger, Thomas; Hajek, Michael; Bilski, Pawel; Körner, Christine; Vanhavere, Filip; Reitz, Günther

    2012-05-01

    In the frame of the EXPOSE-E mission on the Columbus external payload facility EuTEF on board the International Space Station, passive thermoluminescence dosimeters were applied to measure the radiation exposure of biological samples. The detectors were located either as stacks next to biological specimens to determine the depth dose distribution or beneath the sample carriers to determine the dose levels for maximum shielding. The maximum mission dose measured in the upper layer of the depth dose part of the experiment amounted to 238±10 mGy, which relates to an average dose rate of 408±16 μGy/d. In these stacks of about 8 mm height, the dose decreased by 5-12% with depth. The maximum dose measured beneath the sample carriers was 215±16 mGy, which amounts to an average dose rate of 368±27 μGy/d. These values are close to those assessed for the interior of the Columbus module and demonstrate the high shielding of the biological experiments within the EXPOSE-E facility. Besides the shielding by the EXPOSE-E hardware itself, additional shielding was experienced by the external structures adjacent to EXPOSE-E, such as EuTEF and Columbus. This led to a dose gradient over the entire exposure area, from 215±16 mGy for the lowest to 121±6 mGy for maximum shielding. Hence, the doses perceived by the biological samples inside EXPOSE-E varied by 70% (from lowest to highest dose). As a consequence of the high shielding, the biological samples were predominantly exposed to galactic cosmic heavy ions, while electrons and a significant fraction of protons of the radiation belts and solar wind did not reach the samples.

  3. Cosmic Radiation Exposure of Biological Test Systems During the EXPOSE-E Mission

    PubMed Central

    Hajek, Michael; Bilski, Pawel; Körner, Christine; Vanhavere, Filip; Reitz, Günther

    2012-01-01

    Abstract In the frame of the EXPOSE-E mission on the Columbus external payload facility EuTEF on board the International Space Station, passive thermoluminescence dosimeters were applied to measure the radiation exposure of biological samples. The detectors were located either as stacks next to biological specimens to determine the depth dose distribution or beneath the sample carriers to determine the dose levels for maximum shielding. The maximum mission dose measured in the upper layer of the depth dose part of the experiment amounted to 238±10 mGy, which relates to an average dose rate of 408±16 μGy/d. In these stacks of about 8 mm height, the dose decreased by 5–12% with depth. The maximum dose measured beneath the sample carriers was 215±16 mGy, which amounts to an average dose rate of 368±27 μGy/d. These values are close to those assessed for the interior of the Columbus module and demonstrate the high shielding of the biological experiments within the EXPOSE-E facility. Besides the shielding by the EXPOSE-E hardware itself, additional shielding was experienced by the external structures adjacent to EXPOSE-E, such as EuTEF and Columbus. This led to a dose gradient over the entire exposure area, from 215±16 mGy for the lowest to 121±6 mGy for maximum shielding. Hence, the doses perceived by the biological samples inside EXPOSE-E varied by 70% (from lowest to highest dose). As a consequence of the high shielding, the biological samples were predominantly exposed to galactic cosmic heavy ions, while electrons and a significant fraction of protons of the radiation belts and solar wind did not reach the samples. Key Words: Space radiation—Dosimetry—Passive radiation detectors—Thermoluminescence—EXPOSE-E. Astrobiology 12, 387–392. PMID:22680685

  4. Characteristics of Twenty-Nine Aerosol Samplers Tested at U.S. Army Edgewood Chemical Biological Center (2000-2006)

    DTIC Science & Technology

    2011-02-01

    and biological particles in the size range of 0.5 - 13 urn. None of the samplers were tested with all particle sizes . A comparative ranking...dependent on particle aerodynamic size and wind speed. Inlets intended for use either in calm air or indoors can be characterized in an aerosol...on particle size , density, charge, composition, and biofactors. There has been ambiguity in the use of these efficiency terms in the literature. In

  5. [Predictive values of the usual biologic tests for the detection of human immunodeficiency virus infection. Consequences for screening].

    PubMed

    Grémy, F; Salmi, L R

    1995-02-01

    This paper tries to review what is scientifically known about the predictive values of biological tests of HIV infection. The epidemiological situation for that infection is characterized by two facts: the very high values of sensitivity and specificity which are close to unity; the prevalence of seropositivity which is on average--at least in western countries--, very low (except for some small specific groups). Under those conditions, Negative Predictive Values are always very close to unity, and the percentage of false negative tests is extremely low. Things are quite different for Positive Predictive Value, which varies very rapidly with very small shifts or uncertainties about specificity and prevalence. In the case when prevalence is very low (general population screening) and at the same time specificity is not excellent (that means < 0.99 or even < 0.995), Positive Predictive Value is very poor and the proportion of false positive tests rather important. Indeed the analysis of scientific literature, using the method of "best synthesis evidence", reveals numerous discrepancies as to the value of specificity among different tests. Figures vary a lot from one study to another. It is not obvious which screening strategies are concerned by the results, which finally entail a strong statistical uncertainty. Finally, the figures published in the literature are given by high standard laboratories. One may fear the tests realized in routine laboratories are less reliable. As a conclusion, let us say that despite their very good quality, the biological tests, when used separately, should not be trusted without strong previous criticism when applied to samples of the general population. Any biological screening should be preceded by a clinical examination, including a precise inquiry, in order to detect people at risk, that means with a high prior probability. Clinical dialogue has moreover another great interest: it allows health consulting and education, and calls

  6. Cooperative Effects in Biological Suspensions: From Filaments to Propellers

    NASA Astrophysics Data System (ADS)

    Pagonabarraga, I.; Llopis, I.

    We analyze the role of hydrodynamic cooperativity in different systems of biological interest. We describe alternative approaches to model the dynamics of suspensions which account for realistic dynamic coupling on the length and time sales in which mesoscopic suspended particles (such as semiflexible filaments and swimmers) evolve. The time evolution and transport of such systems, which are relevant in physical biology, are studied in detail.

  7. Test Results of Air-Permeable Charcoal Impregnated Suits to Challenge by Chemical and Biological Warfare Agents and Simulants. Executive Summary and Summary Report

    DTIC Science & Technology

    2003-05-01

    proteCt in a "CW ( chemical warfare ) and BW (biological warfare )" agents environment. Swatches of material from each suit design were tested for...factors were determined for each suit. 14. SUBJECT TERMS 15. NUMBER OF PAGES HD Swatch testing Permeation testing 63 GB Chemical protective suits... Testing Procedures This testing was conducted to measure the permeation of chemical agents GB

  8. Developing Achievement Test: A Research for Assessment of 5th Grade Biology Subject

    ERIC Educational Resources Information Center

    Sener, Nilay; Tas, Erol

    2017-01-01

    The purpose of this study is to prepare a multiple-choice achievement test with high reliability and validity for the "Let's Solve the Puzzle of Our Body" unit. For this purpose, a multiple choice achievement test consisting of 46 items was applied to 178 fifth grade students in total. As a result of the test and material analysis…

  9. Cold Regions Environmental Test of Nuclear, Biological, and Chemical Decontamination Equipment

    DTIC Science & Technology

    2007-11-02

    6502, Engine, Cold-starting and Warmup Tests. (2) Decontaminant mixing/filling. Evaluate ease of filling and mixing decontaminants at low temperatures...2. TOP 2-2-650, Engine Cold-Starting and Warmup Tests, 18 July 1980. 3. TOP 8-4-015, Cold Regions Logistics, Supportability Testing of Chemical

  10. 76 FR 36019 - Amendments to Sterility Test Requirements for Biological Products

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-21

    ... as incubation conditions (time and temperature) to be used during testing, suitable test organisms...) and incubation conditions (time and temperature) to be used during testing, with exceptions provided... temperature) and visual examination requirements currently prescribed in Sec. 610.12. Because we propose to...

  11. Mortality follow-up of veterans who participated in military chemical and biological warfare agent testing between 1962 and 1972.

    PubMed

    Kang, Han K; Bullman, Tim

    2009-01-01

    Between 1962 and 1972, several thousand U.S. Navy personnel participated in Project SHAD (Shipboard Hazard and Defense). These tests potentially exposed participants to either active chemical or biological warfare agents or their simulants. This study examined mortality risk associated with participating in SHAD tests by comparing the cause-specific mortality of 4927 SHAD veterans to that of 10,927 other Navy veterans. Compared to other Navy veterans, SHAD veterans had an increased risk of overall mortality, which was due primarily to heart disease deaths.

  12. A versatile system for biological and soil chemical tests on a planetary landing craft. I - Scientific objectives

    NASA Technical Reports Server (NTRS)

    Radmer, R. J.; Kok, B.; Martin, J. P.

    1976-01-01

    We describe an approach for the remote detection and characterization of life in planetary soil samples. A mass spectrometer is used as the central sensor to monitor changes in the gas phase in eleven test cells filled with soil. Many biological assays, ranging from general 'in situ' assays to specific metabolic processes (such as photosynthesis, respiration, denitrification, etc.) can be performed by appropriate additions to the test cell via attached preloaded injector capsules. The system is also compatible with a number of chemical assays such as the analysis of atmospheric composition (both chemical and isotopic), the status of soil water, and the determination of compounds of carbon, nitrogen and sulfur in the soil.

  13. A versatile system for biological and soil chemical tests on a planetary landing craft. I - Scientific objectives

    NASA Technical Reports Server (NTRS)

    Radmer, R. J.; Kok, B.; Martin, J. P.

    1976-01-01

    We describe an approach for the remote detection and characterization of life in planetary soil samples. A mass spectrometer is used as the central sensor to monitor changes in the gas phase in eleven test cells filled with soil. Many biological assays, ranging from general 'in situ' assays to specific metabolic processes (such as photosynthesis, respiration, denitrification, etc.) can be performed by appropriate additions to the test cell via attached preloaded injector capsules. The system is also compatible with a number of chemical assays such as the analysis of atmospheric composition (both chemical and isotopic), the status of soil water, and the determination of compounds of carbon, nitrogen and sulfur in the soil.

  14. The Silicon Trypanosome: a test case of iterative model extension in systems biology

    PubMed Central

    Achcar, Fiona; Fadda, Abeer; Haanstra, Jurgen R.; Kerkhoven, Eduard J.; Kim, Dong-Hyun; Leroux, Alejandro E.; Papamarkou, Theodore; Rojas, Federico; Bakker, Barbara M.; Barrett, Michael P.; Clayton, Christine; Girolami, Mark; Luise Krauth-Siegel, R.; Matthews, Keith R.; Breitling, Rainer

    2016-01-01

    The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome (SilicoTryp) is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology. PMID:24797926

  15. The silicon trypanosome: a test case of iterative model extension in systems biology.

    PubMed

    Achcar, Fiona; Fadda, Abeer; Haanstra, Jurgen R; Kerkhoven, Eduard J; Kim, Dong-Hyun; Leroux, Alejandro E; Papamarkou, Theodore; Rojas, Federico; Bakker, Barbara M; Barrett, Michael P; Clayton, Christine; Girolami, Mark; Krauth-Siegel, R Luise; Matthews, Keith R; Breitling, Rainer

    2014-01-01

    The African trypanosome, Trypanosoma brucei, is a unicellular parasite causing African Trypanosomiasis (sleeping sickness in humans and nagana in animals). Due to some of its unique properties, it has emerged as a popular model organism in systems biology. A predictive quantitative model of glycolysis in the bloodstream form of the parasite has been constructed and updated several times. The Silicon Trypanosome is a project that brings together modellers and experimentalists to improve and extend this core model with new pathways and additional levels of regulation. These new extensions and analyses use computational methods that explicitly take different levels of uncertainty into account. During this project, numerous tools and techniques have been developed for this purpose, which can now be used for a wide range of different studies in systems biology.

  16. Critique of Test Methodologies for Biological Agent Detection and Identification Systems for Military and First Responders

    DTIC Science & Technology

    2002-01-01

    Bacillus cereus and Bacillus thuringiensis (BT). This is of critical importance as these are very common in the soil and the BT is common used to kill...Assays, generic DNA , and Luminescence) have demonstrated significant performance differences when evaluated with common environmental samples...study, salt, sugars, detergents, talc, phosphates, cross-reacting organisms ( Bacillus spp), non-toxic material of biological origin (cereal), as

  17. Testing biological liquid samples using modified m-line spectroscopy method

    NASA Astrophysics Data System (ADS)

    Augusciuk, Elzbieta; Rybiński, Grzegorz

    2005-09-01

    Non-chemical method of detection of sugar concentration in biological (animal and plant source) liquids has been investigated. Simplified set was build to show the easy way of carrying out the survey and to make easy to gather multiple measurements for error detecting and statistics. Method is suggested as easy and cheap alternative for chemical methods of measuring sugar concentration, but needing a lot effort to be made precise.

  18. Protozoan parasites in group-living primates: testing the biological island hypothesis.

    PubMed

    Chapman, Colin A; Bowman, Dwight D; Ghai, Ria R; Gogarten, Jan F; Goldberg, Tony L; Rothman, Jessica M; Twinomugisha, Dennis; Walsh, Chesley

    2012-06-01

    A series of articles by W.J. Freeland published in the 1970s proposed that social organization and behavioral processes were heavily influenced by parasitic infections, which led to a number of intriguing hypotheses concerning how natural selection might act on social factors because of the benefits of avoiding parasite infections. For example, Freeland [1979] showed that all individuals within a given group harbored identical gastrointestinal protozoan faunas, which led him to postulate that social groups were akin to "biological islands" and suggest how this isolation could select specific types of ranging and dispersal patterns. Here, we reexamine the biological island hypothesis by quantifying the protozoan faunas of the same primate species examined by Freeland in the same location; our results do not support this hypothesis. In contrast, we quantified two general changes in protozoan parasite community of primates in the study area of Kibale National Park, Uganda, over the nearly 35 years between sample collections: (1) the colobines found free of parasites in the early 1970s are now infected with numerous intestinal protozoan parasites and (2) groups are no longer biological islands in terms of their protozoan parasites. Whatever the ultimate explanation for these changes, our findings have implications for studies proposing selective forces shaping primate behavior and social organization. © 2011 Wiley Periodicals, Inc.

  19. Instrument for controlling the application of mechanical loads to biological and bicompatible test subjects

    DOEpatents

    Lintilhac, Phillip M.; Vesecky, Thompson B.

    1995-01-01

    Apparatus and methods are disclosed facilitating the application of forces and measurement of dimensions of a test subject. In one arrangement the test subject is coupled to a forcing frame and controlled forces applied thereto. Force applied to the test subject is measured and controlled. A dimensional characteristic of the test subject, such as growth, is measured by a linear variable differential transformer. The growth measurement data can be used to control the force applied. The transducer module receives force and dimensional data from the forcing frame. The transducer module is a separate, microprocessor-based unit that communicates the test data to a controller unit that controls the application of force to the test subject and receives the test data from the transducer module for force control, storage, and/or communication to the user.

  20. Instrument for controlling the application of mechanical loads to biological and bicompatible test subjects

    DOEpatents

    Lintilhac, P.M.; Vesecky, T.B.

    1995-09-19

    An apparatus and methods are disclosed facilitating the application of forces and measurement of dimensions of a test subject. In one arrangement the test subject is coupled to a forcing frame and controlled forces applied thereto. Force applied to the test subject is measured and controlled. A dimensional characteristic of the test subject, such as growth, is measured by a linear variable differential transformer. The growth measurement data can be used to control the force applied. The transducer module receives force and dimensional data from the forcing frame. The transducer module is a separate, microprocessor-based unit that communicates the test data to a controller unit that controls the application of force to the test subject and receives the test data from the transducer module for force control, storage, and/or communication to the user. 8 figs.

  1. Fully printable transparent monolithic solid-state dye-sensitized solar cell with mesoscopic indium tin oxide counter electrode.

    PubMed

    Yang, Ying; Ri, Kwangho; Rong, Yaoguang; Liu, Linfeng; Liu, Tongfa; Hu, Min; Li, Xiong; Han, Hongwei

    2014-09-07

    We present a new transparent monolithic mesoscopic solid-state dye-sensitized solar cell based on trilamellar films of mesoscopic TiO2 nanocrystalline photoanode, a ZrO2 insulating layer and an indium tin oxide counter electrode (ITO-CE), which were screen-printed layer by layer on a single substrate. When the thickness of the ITO-CE was optimized to 2.1 μm, this very simple and fully printable solid-state DSSC with D102 dye and spiro-OMeTAD hole transport materials presents efficiencies of 1.73% when irradiated from the front side and 1.06% when irradiated from the rear side under a standard simulated sunlight condition (AM 1.5 Global, 100 mW cm(-2)). Higher parameters could be expected with a better transparent mesoscopic counter electrode and hole conductor for the printable monolithic mesoscopic solid-state DSSC.

  2. PREFACE: Advanced many-body and statistical methods in mesoscopic systems

    NASA Astrophysics Data System (ADS)

    Anghel, Dragos Victor; Sabin Delion, Doru; Sorin Paraoanu, Gheorghe

    2012-02-01

    It has increasingly been realized in recent times that the borders separating various subfields of physics are largely artificial. This is the case for nanoscale physics, physics of lower-dimensional systems and nuclear physics, where the advanced techniques of many-body theory developed in recent times could provide a unifying framework for these disciplines under the general name of mesoscopic physics. Other fields, such as quantum optics and quantum information, are increasingly using related methods. The 6-day conference 'Advanced many-body and statistical methods in mesoscopic systems' that took place in Constanta, Romania, between 27 June and 2 July 2011 was, we believe, a successful attempt at bridging an impressive list of topical research areas: foundations of quantum physics, equilibrium and non-equilibrium quantum statistics/fractional statistics, quantum transport, phases and phase transitions in mesoscopic systems/superfluidity and superconductivity, quantum electromechanical systems, quantum dissipation, dephasing, noise and decoherence, quantum information, spin systems and their dynamics, fundamental symmetries in mesoscopic systems, phase transitions, exactly solvable methods for mesoscopic systems, various extension of the random phase approximation, open quantum systems, clustering, decay and fission modes and systematic versus random behaviour of nuclear spectra. This event brought together participants from seventeen countries and five continents. Each of the participants brought considerable expertise in his/her field of research and, at the same time, was exposed to the newest results and methods coming from the other, seemingly remote, disciplines. The talks touched on subjects that are at the forefront of topical research areas and we hope that the resulting cross-fertilization of ideas will lead to new, interesting results from which everybody will benefit. We are grateful for the financial and organizational support from IFIN-HH, Ovidius

  3. Concurrent use of REM latency, dexamethasone suppression, clonidine, and apomorphine tests as biological markers of endogenous depression: a pilot study.

    PubMed

    Ansseau, M; Scheyvaerts, M; Doumont, A; Poirrier, R; Legros, J J; Franck, G

    1984-07-01

    In a sample of 12 major depressive inpatients, endogenous subtype (8 primary and 4 secondary) defined by Research Diagnostic Criteria, we compared the sensitivity of four potential biological markers: latency of rapid eye movement (REM) sleep (recorded during at least 4 consecutive nights), dexamethasone suppression, and the clonidine and apomorphine tests. Shortened REM latency (less than 50 minutes during at least 1 night) identified 67% of depressives (87% of primary and 25% of secondary); nonsuppression after dexamethasone identified 50% of depressives (62% of primary and 25% of secondary); blunted growth hormone (GH) response after clonidine identified 75% of depressives (100% of primary and 25% of secondary); and blunted GH response after apomorphine identified 42% of depressives (62% of primary and 0% of secondary). Ninety-two percent of patients were correctly identified by at least one biological marker (100% of primary and 75% of secondary depressives). Of 67% of patients positive on at least two biological markers, all were primary depressives (100%). These four biological markers do not necessarily identify the same population, suggesting that their concurrent use may yield the highest level of diagnostic sensitivity.

  4. Full printable processed mesoscopic CH₃NH₃PbI₃/TiO₂ heterojunction solar cells with carbon counter electrode.

    PubMed

    Ku, Zhiliang; Rong, Yaoguang; Xu, Mi; Liu, Tongfa; Han, Hongwei

    2013-11-04

    A mesoscopic methylammonium lead iodide (CH₃NH₃PbI₃) perovskite/TiO₂ heterojunction solar cell is developed with low-cost carbon counter electrode (CE) and full printable process. With carbon black/spheroidal graphite CE, this mesoscopic heterojunction solar cell presents high stability and power conversion efficiency of 6.64%, which is higher than that of the flaky graphite based device and comparable to the conventional Au version.

  5. 'Battling my biology': psychological effects of genetic testing for risk of weight gain.

    PubMed

    Meisel, S F; Wardle, J

    2014-04-01

    The availability of genetic tests for multifactorial conditions such as obesity raises concerns that higher-risk results could lead to fatalistic reactions or lower-risk results to complacency. No study has investigated the effects of genetic test feedback for the risk of obesity in non-clinical samples. The present study explored psychological and behavioral reactions to genetic test feedback for a weight related gene (FTO) in a volunteer sample (n = 18) using semi-structured interviews. Respondents perceived the gene test result as scientifically objective; removing some of the emotion attached to the issue of weight control. Those who were struggling with weight control reported relief of self-blame. There was no evidence for either complacency or fatalism; all respondents emphasized the importance of lifestyle choices in long-term weight management, although they recognized the role of both genes and environment. Regardless of the test result, respondents evaluated the testing positively and found it motivating and informative. Genetic test feedback for risk of weight gain may offer psychological benefits beyond its objectively limited clinical utility. As the role of genetic counselors is likely to expand, awareness of reasons for genetic testing for common, complex conditions and reactions to the test result is important.

  6. Mesoscopic modeling of cancer photothermal therapy using single-walled carbon nanotubes and near infrared radiation: insights through an off-lattice Monte Carlo approach

    NASA Astrophysics Data System (ADS)

    Gong, Feng; Hongyan, Zhang; Papavassiliou, Dimitrios V.; Bui, Khoa; Lim, Christina; Duong, Hai M.

    2014-05-01

    Single-walled carbon nanotubes (SWNTs) are promising heating agents in cancer photothermal therapy when under near infrared radiation, yet few efforts have been focused on the quantitative understanding of the photothermal energy conversion in biological systems. In this article, a mesoscopic study that takes into account SWNT morphologies (diameter and aspect ratio) and dispersions (orientation and concentration), as well as thermal boundary resistance, is performed by means of an off-lattice Monte Carlo simulation. Results indicate that SWNTs with orientation perpendicular to the laser, smaller diameter and better dispersion have higher heating efficiency in cancer photothermal therapy. Thermal boundary resistances greatly inhibit thermal energy transfer away from SWNTs, thereby affecting their heating efficiency. Through appropriate interfacial modification around SWNTs, compared to the surrounding healthy tissue, a higher temperature of the cancer cell can be achieved, resulting in more effective cancer photothermal therapy. These findings promise to bridge the gap between macroscopic and microscopic computational studies of cancer photothermal therapy.

  7. Biological-mechanical waste treatment tests at a landfill in East Germany

    SciTech Connect

    Wotte, J.; Brummack, J.; Paar, S.; Gemende, B.

    1996-11-01

    The paper begins by describing the present situation in East Germany with regard to sanitary landfills, that is, there is very limited space for new landfills. The paper discusses the new German waste act amendments, special waste management problems in East Germany, and the combination biological and mechanical waste treatment (BMT) method proposed to help solve these problems. In general terms the BMT method would use a combination of composting, fermentation, separation, mixing, and crushing processes to minimize the waste to be disposed of and to render it harmless to further degradation which leads to emission of methane and contaminated leachates from the landfills.

  8. Biological testing of sediment for the Olympia Harbor Navigation Improvement Project, 1988: Geoduck, amphipod, and echinoderm bioassays

    SciTech Connect

    Ward, J.A.; Word, J.Q.; Antrim, L.D.

    1989-05-01

    The Olympia Harbor Navigation Improvement Project requires the dredging of approximately 330,000 cubic yards (cy) of sediment from the harbor entrance channel and 205,185 cy from the turning basin. Puget Sound Dredged Disposal Analysis (PSDDA) partial characterization studies were used to plan a full sediment characterization in which chemical analyses and biological testing of sediments evaluated the suitability of the dredged material for unconfined, open-water disposal. The US Army Corps of Engineers (COE), Seattle District, contracted with NOAA/NMFS, Environmental Conservation Division, to perform the chemical analysis and Microtox bioassay tests, and with the Battelle/Marine Sciences Laboratory (MSL) in Sequim to perform flow-through solid-phase bioassays utilizing juvenile (8 to 10 mm) geoduck clams, Panopea generosa, and static solid phase bioassays using the phoxocephalid amphipod, Rhepoxynius abronius, developing embryos and gametes of the purple sea urchin, Strongylocentrotus purpuratus, and the larvae of the Pacific oyster Crassostrea gigas. When the results of the biological tests were evaluated under PSDDA guidelines, it was found that all the tested sediment treatments from Olympia Harbor are suitable for unconfined open-water disposal. 14 refs., 12 figs., 3 tabs.

  9. Biological alternatives to chemical identification for the ecotoxicological assessment of industrial effluents: The RTG-2 in vitro cytotoxicity test

    SciTech Connect

    Castano, A. . Centro de Sanidad Ambiental); Vega, M.; Blazquez, T.; Tarazona, J.V. )

    1994-10-01

    Ecotoxicology is concerned with the effects of chemicals on biological systems. Identifying components of complex aqueous effluents poses special problems, and can be useless if there is a lack of information on the biological effects of the identified chemicals. Toxicity-based (bioassay-directed) sample fractionation can be very useful, but the small amount of fractioned material is a constraint that can be solved by using in vitro tests. The RTG-2 in vitro cytotoxicity test has been used to assess (a) the efficacy of a treatment plant in the aeronautics industry and (b) the exposure of fish and molluscs cultured in Esteiro Bay to the effluent of a fish-processing factory. Ecotoxicological assessments could be done without identifying the responsible chemicals. The RTG-2 test was used in combination with concentration/fractionation procedures. It proved that the toxicity of the liquid wastes from the aeronautics industry was eliminated by the treatment, and that molluscs and fish reared in Esteiro Bay had accumulated toxic chemicals dumped by the fish-processing factory. A combination of the RTG-2 cytotoxicity test and HPLC proved to give useful information even for chemicals not identified by GC-MS.

  10. Experimental Work in Biology: Book 1, Food Tests; Book 2, Enzymes; Book 3, Soil.

    ERIC Educational Resources Information Center

    Mackean, D. G.

    Laboratory experiments are presented in these first three manuals of a six-volume series for use at the 12- to 16-year-old, or British CSE, level. On the subject of food tests, 17 exercises are prepared in connection with Biuret reactions, starch and emulsion tests, Millon's and Benedict's reagents, reagent sensitivity, and calorific values and…

  11. Experimental Work in Biology: Book 1, Food Tests; Book 2, Enzymes; Book 3, Soil.

    ERIC Educational Resources Information Center

    Mackean, D. G.

    Laboratory experiments are presented in these first three manuals of a six-volume series for use at the 12- to 16-year-old, or British CSE, level. On the subject of food tests, 17 exercises are prepared in connection with Biuret reactions, starch and emulsion tests, Millon's and Benedict's reagents, reagent sensitivity, and calorific values and…

  12. Alignment between High School Biology Curriculum Standard and the Standardised Tests of Four Provinces in China

    ERIC Educational Resources Information Center

    Lu, Qun; Liu, Enshan

    2012-01-01

    With the development and implementation of new curriculum standards, the field tests of education reform in senior high schools began in 2004 in four pilot provinces in mainland China. After five years of the reform, it is necessary to know how and to what extent the curriculum standard guides test classroom instruction. The present study was…

  13. Alignment between High School Biology Curriculum Standard and the Standardised Tests of Four Provinces in China

    ERIC Educational Resources Information Center

    Lu, Qun; Liu, Enshan

    2012-01-01

    With the development and implementation of new curriculum standards, the field tests of education reform in senior high schools began in 2004 in four pilot provinces in mainland China. After five years of the reform, it is necessary to know how and to what extent the curriculum standard guides test classroom instruction. The present study was…

  14. Euglena gracilis as a supplementary test organism for detecting biologically active compounds.

    PubMed

    Macor, M; Beno, J; Grones, J; Siekel, P; Novotný, J

    1996-01-01

    The mutagenic activity of more than 120 antimicrobial agents and protective components was investigated. Only Kathon showed a consistent increase in revertant counts in the Ames test on Salmonella typhimurium. The hereditary bleaching test on Euglena gracilis used for detecting extranuclear mutations, showed positive results for Kathon, triethanolamine and diamine silver tetraborate.

  15. 40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... effect until the revised testing guidelines are published as final regulations. (a) No single test or approach can be applied in all cases to evaluate the effects of proposed discharges of dredged or fill... effects. The principal concerns of discharge of dredged or fill material that contain contaminants are the...

  16. 40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... effect until the revised testing guidelines are published as final regulations. (a) No single test or approach can be applied in all cases to evaluate the effects of proposed discharges of dredged or fill... effects. The principal concerns of discharge of dredged or fill material that contain contaminants are the...

  17. Planar biaxial testing of soft biological tissue using rakes: A critical analysis of protocol and fitting process.

    PubMed

    Fehervary, Heleen; Smoljkić, Marija; Vander Sloten, Jos; Famaey, Nele

    2016-08-01

    Mechanical characterization of soft biological tissue is becoming more and more prevalent. Despite the growing use of planar biaxial testing for soft tissue characterization, testing conditions and subsequent data analysis have not been standardized and vary widely. This also influences the quality of the result of the parameter fitting. Moreover, the testing conditions and data analysis are often not or incompletely reported, which impedes the proper comparison of parameters obtained from different studies. With a focus on planar biaxial tests using rakes, this paper investigates varying testing conditions and varying data analysis methods and their effect on the quality of the parameter fitting results. By means of a series of finite element simulations, aspects such as number of rakes, rakes׳ width, loading protocol, constitutive model, material stiffness and anisotropy are evaluated based on the degree of homogeneity of the stress field, and on the correlation between the experimentally obtained stress and the stress derived from the constitutive model. When calculating the aforementioned stresses, different definitions of the section width and deformation gradient are used in literature, each of which are looked into. Apart from this degree of homogeneity and correlation, also the effect on the quality of the parameter fitting result is evaluated. The results show that inhomogeneities can be reduced to a minimum for wise choices of testing conditions and analysis methods, but never completely eliminated. Therefore, a new parameter optimization procedure is proposed that corrects for the inhomogeneities in the stress field and induces significant improvements to the fitting results. Recommendations are made for best practice in rake-based planar biaxial testing of soft biological tissues and subsequent parameter fitting, and guidelines are formulated for reporting thereof in publications.

  18. Proposed biological testing methods for the United States incineration-at-sea research program

    SciTech Connect

    Strobel, C.J.; Gentile, J.H.; Schimmel, S.C.; Carr, R.S.; Williams, J.W.

    1988-01-01

    As part of the United States Environmental Protection Agency's Incineration-at-Sea research program, a suite of toxicity tests has been selected for assessing the toxicity of incinerator emissions generated during the combustion of chlorinated wastes. The test organisms for the five short-term chronic tests are the inland silverside, Menidia beryllina, the myside Mysidopsis bahia, the red macroalga Champia parvula, the polychaete Dinophilus gyrociliatus, and gametes from the sea urchin Arbacia punctulata. The durations of individual tests range from 2 hours to 7 days. The endpoints include survival, growth and reproductive effects. The results have demonstrated that the proposed methodologies can be used to test the toxicity of gaseous emissions, and that there appears to be no significant toxicity associated with the combustion products of a carrier fuel oil.

  19. Nanostructured Interfaces for Organized Mesoscopic Biotic-Abiotic Materials

    DTIC Science & Technology

    2011-09-30

    material for lithium batteries and solar cells . Previously, the proteins silicatein, lysozyme, silaffins, and amino- acids have been employed for...a fundamental basis for prospective ultra-sensing platform from hybrid organized nanomaterials for chemical, optical, and biological applications...with potential for dramatic miniaturization and superior sensitivity of lightweight hybrid sensor arrays. Students trained in this field will form a

  20. Effect of chemical and biological surfactants on activated sludge of MBR system: microscopic analysis and foam test.

    PubMed

    Capodici, Marco; Di Bella, Gaetano; Nicosia, Salvatore; Torregrossa, Michele

    2015-02-01

    A bench-scale MBR unit was operated, under stressing condition, with the aim of stimulating the onset of foaming in the activated sludge. Possible synergies between synthetic surfactants in the wastewater and biological surfactants (Extra-Cellular Polymeric Substances, EPSs) were investigated by changing C/N ratio. The growth of filamentous bacteria was also discussed. The MBR unit provided satisfactory overall carbon removal overall efficiencies: in particular, synthetic surfactants were removed with efficiency higher than 90% and 95% for non-ionic and ionic surfactants, respectively. Lab investigation suggested also the importance to reduce synthetic surfactants presence entering into mixed liquor: otherwise, their presence can significantly worsen the natural foaming caused by biological surfactants (EPSs) produced by bacteria. Finally, a new analytic method based on "ink test" has been proposed as a useful tool to achieve a valuation of EPSs bound fraction. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Single and multiple streamer DBD micro-discharges for testing inactivation of biologically contaminated surfaces

    NASA Astrophysics Data System (ADS)

    Prukner, Vaclav; Dolezalova, Eva; Simek, Milan

    2014-10-01

    Highly reactive environment produced by atmospheric-pressure, non-equilibrium plasmas generated by surface dielectric barrier discharges (SDBDs) may be used for inactivation of biologically contaminated surfaces. We investigated decontamination efficiency of reactive environment produced by single/multiple surface streamer micro-discharge driven by amplitude-modulated AC power in coplanar electrode geometry on biologically contaminated surface by Escherichia coli. The discharges were fed by synthetic air with water vapor admixtures at atmospheric pressure, time of treatment was set from 10 second to 10 minutes, diameters of used SDBD electrodes (single and multiple streamer) and homogeneously contaminated disc samples were equal (25 mm), the distance between the electrode and contaminated surface was 2 mm. Both a conventional cultivation and fluorescent method LIVE/DEAD Bacterial Viability kit were applied to estimate counts of bacteria after the plasma treatment. Inactivation was effective and bacteria partly lost ability to grow and became injured and viable/active but non-cultivable (VBNC/ABNC). Work was supported by the MEYS under Project LD13010, VES13 COST CZ (COST Action MP 1101).

  2. A test of Ockham's razor: implications of conjugated linoleic acid in bone biology.

    PubMed

    Watkins, Bruce A; Li, Yong; Lippman, Hugh E; Reinwald, Susan; Seifert, Mark F

    2004-06-01

    The philosopher William of Ockham is recognized for the maxim that an assumption introduced to explain a phenomenon must not be multiplied beyond necessity, or that the simplest explanation is probably the correct explanation. The general truth is that conjugated linoleic acids (CLAs) are nutrients. However, the demonstration that these isomers of octadecadienoic acid protect against cancers in rodents stimulated curiosity that directed significant resources to characterize the biological functions of these fatty acids in cell and animal models. The benefits to human subjects given supplements of CLA were at best modest. The disappointing results in humans should be taken as an opportunity to critically evaluate all findings of CLA use and to consolidate the common actions of this nutrient so that future investigations focus on specific isomers and the most reasonable mechanisms. As such, the principal and consistently reported benefits of CLA have been in improving cancer outcomes, reducing body fat in growing animals, and modulating cell functions. Recognizing where related actions of CLA converge in specific disease conditions and physiologic states is how research efforts should be directed to minimize the pursuit of superfluous theories. Here, we briefly review the current biological effects of CLA and attempt to integrate their potential effect on the physiology and health of the skeletal system. Thus, the purpose of this review is to advance the science of CLA and to identify areas of research in which these nutrients affect bone metabolism and skeletal health.

  3. The relationship between agricultural intensification and biological control: experimental tests across Europe.

    PubMed

    Thies, Carsten; Haenke, Sebastian; Scherber, Christoph; Bengtsson, Janne; Bommarco, Riccardo; Clement, Lars W; Ceryngier, Piotr; Dennis, Christopher; Emmerson, Mark; Gagic, Vesna; Hawro, Violetta; Liira, Jaan; Weisser, Wolfgang W; Winqvist, Camilla; Tscharntke, Teja

    2011-09-01

    Agricultural intensification can affect biodiversity and related ecosystem services such as biological control, but large-scale experimental evidence is missing. We examined aphid pest populations in cereal fields under experimentally reduced densities of (1) ground-dwelling predators (-G), (2) vegetation-dwelling predators and parasitoids (-V), (3) a combination of (1) and (2) (-G-V), compared with open-fields (control), in contrasting landscapes with low vs. high levels of agricultural intensification (AI), and in five European regions. Aphid populations were 28%, 97%, and 199% higher in -G, -V, and -G-V treatments, respectively, compared to the open fields, indicating synergistic effects of both natural-enemy groups. Enhanced parasitoid: host and predator: prey ratios were related to reduced aphid population density and population growth. The relative importance of parasitoids and vegetation-dwelling predators greatly differed among European regions, and agricultural intensification affected biological control and aphid density only in some regions. This shows a changing role of species group identity in diverse enemy communities and a need to consider region-specific landscape management.

  4. Radiotoxicity of gadolinium-148 and radium-223 in mouse testes: relative biological effectiveness of alpha-particle emitters in vivo.

    PubMed

    Howell, R W; Goddu, S M; Narra, V R; Fisher, D R; Schenter, R E; Rao, D V

    1997-03-01

    The biological effects of radionuclides that emit alpha particles are of considerable interest in view of their potential for therapy and their presence in the environment. The present work is a continuation of our ongoing effort to study the radiotoxicity of alpha-particle emitters in vivo using the survival of murine testicular sperm heads as the biological end point. Specifically, the relative biological effectiveness (RBE) of very low-energy alpha particles (3.2 MeV) emitted by 148Gd is investigated and determined to be 7.4 +/- 2.4 when compared to the effects of acute external 120 kVp X rays. This datum, in conjunction with our earlier results for 210Po and 212Pb in equilibrium with its daughters, is used to revise and extend the range of validity of our previous RBE-energy relationship for alpha particles emitted by tissue-incorporated radionuclides. The new empirical relationship is given by RBE alpha = 9.14 - 0.510 E alpha where 3 < E alpha < 9 MeV. The validity of this empirical relationship is tested by determining the RBE of the prolific alpha-particle emitter 223Ra (in equilibrium with its daughters) experimentally in the same biological model and comparing the value obtained experimentally with the predicted value. The resulting RBE values are 5.4 +/- 0.9 and 5.6, respectively. This close agreement strongly supports the adequacy of the empirical RBE-E alpha relationship to predict the biological effects of alpha-particle emitters in vivo.

  5. Radiotoxicity of Gadolinium-148 and Radium-223 in Mouse Testes: Relative Biological Effectiveness of Alpha-Particle Emitters In Vivo

    PubMed Central

    Howell, Roger W.; Goddu, S. Murty; Narra, Venkat R.; Fisher, Darrell R.; Schenter, Robert E.; Rao, Dandamudi V.

    2012-01-01

    The biological effects of radionuclides that emit α particles are of considerable interest in view of their potential for therapy and their presence in the environment. The present work is a continuation of our ongoing effort to study the radiotoxicity of α-particle emitters in vivo using the survival of murine testicular sperm heads as the biological end point. Specifically, the relative biological effectiveness (RBE) of very low-energy α particles (3.2 MeV) emitted by 148Gd is investigated and determined to be 7.4 ± 2.4 when compared to the effects of acute external 120 kVp X rays. This datum, in conjunction with our earlier results for 210Po and 212Pb in equilibrium with its daughters, is used to revise and extend the range of validity of our previous RBE–energy relationship for α particles emitted by tissue-incorporated radionuclides. The new empirical relationship is given by RBEα = 9.14 − 0.510 Eα, where 3 < Eα < 9 MeV. The validity of this empirical relationship is tested by determining the RBE of the prolific α-particle emitter 223Ra (in equilibrium with its daughters) experimentally in the same biological model and comparing the value obtained experimentally with the predicted value. The resulting RBE values are 5.4 ± 0.9 and 5.6, respectively. This close agreement strongly supports the adequacy of the empirical RBE-Eα relationship to predict the biological effects of α-particle emitters in Vivo. PMID:9052681

  6. Multiparticle Correlations in Mesoscopic Scattering: Boson Sampling, Birthday Paradox, and Hong-Ou-Mandel Profiles

    NASA Astrophysics Data System (ADS)

    Urbina, Juan-Diego; Kuipers, Jack; Matsumoto, Sho; Hummel, Quirin; Richter, Klaus

    2016-03-01

    The interplay between single-particle interference and quantum indistinguishability leads to signature correlations in many-body scattering. We uncover these with a semiclassical calculation of the transmission probabilities through mesoscopic cavities for systems of noninteracting particles. For chaotic cavities we provide the universal form of the first two moments of the transmission probabilities over ensembles of random unitary matrices, including weak localization and dephasing effects. If the incoming many-body state consists of two macroscopically occupied wave packets, their time delay drives a quantum-classical transition along a boundary determined by the bosonic birthday paradox. Mesoscopic chaotic scattering of Bose-Einstein condensates is, then, a realistic candidate to build a boson sampler and to observe the macroscopic Hong-Ou-Mandel effect.

  7. Puzzling electron behavior analogous to the Braess paradox in a mesoscopic network

    NASA Astrophysics Data System (ADS)

    Toussaint, Sébastien; Faniel, Sébastien; Martins, Frederico; Pala, Marco; Desplanque, Ludovic; Wallart, Xavier; Huant, Serge; Sellier, Hermann; Bayot, Vincent; Hackens, Benoit

    A counterintuitive behavior analogous to the Braess paradox is encountered in a two-terminal mesoscopic network patterned in a two-dimensional electron system (2DES). Decreasing locally the electron density of one channel in the network paradoxically leads to an increased network conductance. Our scanning gate microscopy experiments reveals this puzzling conductance variation, thanks to tip-induced localized modifications of electron flow throughout the network's channels at low temperature, in the ballistic and coherent regime of transport. We compare the amplitude of the measured anomalous conductance variation with conductance changes induced by other mechanisms at play in the mesoscopic network, such as interference phenomena between different paths, and Coulomb blockade due to disorder-induced localized states. The robustness of this puzzling behavior is inspected by varying the global 2DES density, magnetic field and temperature. S.T. acknowledges support from the Belgian FRS-FNRS (FRIA).

  8. Puzzling electron behavior analogous to the Braess paradox in a mesoscopic networ

    NASA Astrophysics Data System (ADS)

    Toussaint, Sébastien; Faniel, Sébastien; Martins, Frederico; Pala, Marco; Desplanque, Ludovic; Wallart, Xavier; Huant, Serge; Sellier, Hermann; Bayot, Vincent; Hackens, Benoit

    A counterintuitive behavior analogous to the Braess paradox is encountered in a two-terminal mesoscopic network patterned in a two-dimensional electron system (2DES). Decreasing locally the electron density of one channel in the network paradoxically leads to an increased network conductance. Our scanning gate microscopy experiments reveals this puzzling conductance variation, thanks to tip-induced localized modifications of electron flow throughout the network's channels at low temperature, in the ballistic and coherent regime of transport. We compare the amplitude of the measured anomalous conductance variation with conductance changes induced by other mechanisms at play in the mesoscopic network, such as interference phenomena between different paths, and Coulomb blockade due to disorder-induced localized states. The robustness of this puzzling behavior is inspected by varying the global 2DES density, magnetic field and temperature S.T. acknowledges support from the Belgian FRS-FNRS (FRIA).

  9. Fabrication and Optical Properties of Strain-free Self-assembled Mesoscopic GaAs Structures.

    PubMed

    da Silva, Saimon Filipe Covre; Mardegan, Thayná; de Araújo, Sidnei Ramis; Ramirez, Carlos Alberto Ospina; Kiravittaya, Suwit; Couto, Odilon D D; Iikawa, Fernando; Deneke, Christoph

    2017-12-01

    We use a combined process of Ga-assisted deoxidation and local droplet etching to fabricate unstrained mesoscopic GaAs/AlGaAs structures exhibiting a high shape anisotropy with a length up to 1.2 μm and a width of 150 nm. We demonstrate good controllability over size and morphology of the mesoscopic structures by tuning the growth parameters. Our growth method yields structures, which are coupled to a surrounding quantum well and present unique optical emission features. Microscopic and optical analysis of single structures allows us to demonstrate that single structure emission originates from two different confinement regions, which are spectrally separated and show sharp excitonic lines. Photoluminescence is detected up to room temperature making the structures the ideal candidates for strain-free light emitting/detecting devices.

  10. A novel approach for generating giant electronic persistent currents in symmetric defect mesoscopic-ring networks

    NASA Astrophysics Data System (ADS)

    Hu, Xubo; Yang, Xiangbo; Deng, Dongmei

    2017-04-01

    According to optical analogy of electrons' behavior in mesoscopic systems, we change optical symmetric defect waveguide networks being able to create strong photonic localizations into electronic symmetric defect mesoscopic-ring networks (SDMRNs) being capable of generating giant electronic persistent currents. These simple SDMRNs can produce giant electronic persistent currents in the absence of magnetic field, stub, and impurity. We give out the sufficient condition for generating maximum electronic persistent current |Jp|max in SDMRNs and obtain the formula of |Jp|max. It is found that |Jp|max is proportional to the inverse square of the breaking degree of defect, Δd. Our results may deepen one's knowledge on the correlation between photonic and electronic networks and may be useful for the designing of microcircuits with large electric current.

  11. Reproducible mesoscopic superpositions of Bose-Einstein condensates and mean-field chaos

    SciTech Connect

    Gertjerenken, Bettina; Arlinghaus, Stephan; Teichmann, Niklas; Weiss, Christoph

    2010-08-15

    In a parameter regime for which the mean-field (Gross-Pitaevskii) dynamics becomes chaotic, mesoscopic quantum superpositions in phase space can occur in a double-well potential, which is shaken periodically. For experimentally realistic initial states, such as the ground state of some 100 atoms, the emergence of mesoscopic quantum superpositions in phase space is investigated numerically. It is shown to be reproducible, even if the initial conditions change slightly. Although the final state is not a perfect superposition of two distinct phase states, the superposition is reached an order of magnitude faster than in the case of the collapse-and-revival phenomenon. Furthermore, a generator of entanglement is identified.

  12. Local Transport Measurements at Mesoscopic Length Scales Using Scanning Tunneling Potentiometry

    NASA Astrophysics Data System (ADS)

    Wang, Weigang; Munakata, Ko; Rozler, Michael; Beasley, Malcolm R.

    2013-06-01

    Under mesoscopic conditions, the transport potential on a thin film carrying a current is theoretically expected to bear spatial variation due to quantum interference. Scanning tunneling potentiometry is the ideal tool to investigate such variation, by virtue of its high spatial resolution. We report in this Letter the first detailed measurement of transport potential under mesoscopic conditions. Epitaxial graphene at a temperature of 17 K was chosen as the initial system for study because the characteristic transport length scales in this material are relatively large. Tip jumping artifacts are a major possible contribution to systematic errors; and we mitigate such problems by using custom-made slender and sharp tips manufactured by focused ion beam. In our data, we observe residual resistivity dipoles associated with topographical defects, and local peaks and dips in the potential that are not associated with topographical defects.

  13. Quantization, coherent states and geometric phases of a generalized nonstationary mesoscopic RLC circuit

    NASA Astrophysics Data System (ADS)

    Pedrosa, Inácio A.; Melo, Jilvan L.; Salatiel, Sadoque

    2014-11-01

    We present an alternative quantum treatment for a generalized mesoscopic RLC circuit with time-dependent resistance, inductance and capacitance. Taking advantage of the Lewis and Riesenfeld quantum invariant method and using quadratic invariants we obtain exact nonstationary Schrödinger states for this electromagnetic oscillation system. Afterwards, we construct coherent and squeezed states for the quantized RLC circuit and employ them to investigate some of the system's quantum properties, such as quantum fluctuations of the charge and the magnetic flux and the corresponding uncertainty product. In addition, we derive the geometric, dynamical and Berry phases for this nonstationary mesoscopic circuit. Finally we evaluate the dynamical and Berry phases for three special circuits. Surprisingly, we find identical expressions for the dynamical phase and the same formulae for the Berry's phase.

  14. Fabrication and Optical Properties of Strain-free Self-assembled Mesoscopic GaAs Structures

    NASA Astrophysics Data System (ADS)

    da Silva, Saimon Filipe Covre; Mardegan, Thayná; de Araújo, Sidnei Ramis; Ramirez, Carlos Alberto Ospina; Kiravittaya, Suwit; Couto, Odilon D. D.; Iikawa, Fernando; Deneke, Christoph

    2017-01-01

    We use a combined process of Ga-assisted deoxidation and local droplet etching to fabricate unstrained mesoscopic GaAs/AlGaAs structures exhibiting a high shape anisotropy with a length up to 1.2 μm and a width of 150 nm. We demonstrate good controllability over size and morphology of the mesoscopic structures by tuning the growth parameters. Our growth method yields structures, which are coupled to a surrounding quantum well and present unique optical emission features. Microscopic and optical analysis of single structures allows us to demonstrate that single structure emission originates from two different confinement regions, which are spectrally separated and show sharp excitonic lines. Photoluminescence is detected up to room temperature making the structures the ideal candidates for strain-free light emitting/detecting devices.

  15. Mesoscopic Hamiltonian for the fluctuations of adsorbed Lennard-Jones liquid films.

    PubMed

    Fernández, Eva M; Chacón, Enrique; MacDowell, Luis G; Tarazona, Pedro

    2015-06-01

    We use Monte Carlo simulations of a Lennard-Jones fluid adsorbed on a short-range planar wall substrate to study the fluctuations in the thickness of the wetting layer, and we get a quantitative and consistent characterization of their mesoscopic Hamiltonian, H[ξ]. We have observed important finite-size effects, which were hampering the analysis of previous results obtained with smaller systems. The results presented here support an appealing simple functional form for H[ξ], close but not exactly equal to the theoretical nonlocal proposal made on the basis a generic density-functional analysis by Parry and coworkers. We have analyzed systems under different wetting conditions, as a proof of principle for a method that provides a quantitative bridge between the molecular interactions and the phenomenology of wetting films at mesoscopic scales.

  16. Mesoscopic fluctuations of the population of a qubit in a strong alternating field

    SciTech Connect

    Denisenko, M. V. Satanin, A. M.

    2016-12-15

    Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau–Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of the population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.

  17. Mesoscopic fluctuations of the population of a qubit in a strong alternating field

    NASA Astrophysics Data System (ADS)

    Denisenko, M. V.; Satanin, A. M.

    2016-12-01

    Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau-Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of the population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.

  18. Dispersed oil toxicity tests with biological species indigenous to the Gulf of Mexico. Final report

    SciTech Connect

    Fucik, K.W.; Carr, K.A.; Balcom, B.J.

    1994-08-01

    Static and flowthrough aquatic acute toxicity testing protocols were utilized on eggs and larvae of seven commercially important invertebrates and fishes from the Gulf of Mexico. Test organisms were exposed to Central and Western Gulf oils, dispersed oil, and Corexit 9527. Species included brown shrimp (Penaeus aztecus), white shrimp (Penaeus setiferus), blue crab (Callinectes sapidus), eastern oyster (Crassostrea virginica), red drum (Sciaenops ocellatus), inland silverside (Menidia berylina), and spot (Leiosomus xanthurus). Atlantic menhaden (Brevoortia tyrannus) was also tested because gulf menhaden were not available. Mysids (Mysidopsis bahia) were evaluated as part of a chronic toxicity assessment.

  19. [Ethylene oxide sterilization. II. Influence of test devices on the performance of biological monitors and its evaluation].

    PubMed

    Pinto, T de J; Saito, T

    1992-12-01

    In view of the importance of the assurance of the sterility of medical devices, with a large incidence of tubular forms, a study of biological monitors was undertaken, using paper as a carrier, the dimension of the test specimens being the variable considered. After the sterilization process in an industrial cycle, followed by the recovery of the surviving spores through inoculation of the carriers into thioglycolate broth, soybean-casein broth and this last with the addition of bromothymol blue. No differences were found between the growth promoting capacity of these 3 media. The effectiveness of sterilization was dependent on the dimension of the test specimens. The periodic determination of residual gas content on the test specimens, as well as the monitoring of the industrial environment demonstrate the need and importance of the legislation in force.

  20. Mesoscopic transport and interferometry with wave packets of ultracold atoms: Effects of quantum coherence and interactions

    SciTech Connect

    Das, Kunal K.

    2011-09-15

    We propose a way to simulate mesoscopic transport processes with counterpropagating wave packets of ultracold atoms in quasi-one-dimensional (1D) waveguides and show quantitative agreement with analytical results. The method allows the study of a broad range of transport processes at the level of individual modes, not possible in electronic systems. Typically suppressed effects of quantum coherence become manifest, along with the effects of tunable interactions, which can be used to develop a simpler type of sensitive atom interferometer.

  1. Microstructural evolution and irreversibility in the viscoelastic response of mesoscopic dusty-plasma liquids.

    PubMed

    Chan, Chia-Ling; I, Lin

    2007-03-09

    We experimentally demonstrate the viscoelastic response and construct a microscopic dynamical picture using a quasi-2D dusty-plasma liquid confined in a mesoscopic gap and sheared periodically. The correlation between microdisplacement and structural evolution at the discrete kinetic level is explored. Through hopping, the structural rearrangement associated with shear enhanced stretching, kinking, breaking, and reconnection of local lattice lines generates irreversible plastic deformation. The strain energy accumulation in the twisted regions without topological rearrangement is the source for local rebound.

  2. The influence of society's mesoscopic structure on the rate of epidemic spreading

    NASA Astrophysics Data System (ADS)

    Kashisaz, Hadi; Darooneh, Amir H.

    2016-06-01

    In this study, we investigate the role of the mesoscopic structural properties of a scale-free social network on the contagion spreading. We focus on both the exponent of power-law community size distribution function (β) and the mixing parameter (μ). Findings show that increasing β reduces the rate of epidemic spreading. On the other hand, increasing μ increases the rate of epidemic spreading. Two innovating parameters, Temperature and cos θ , are introduced here to analyze these effects.

  3. Continuum Limit of a Mesoscopic Model with Elasticity of Step Motion on Vicinal Surfaces

    NASA Astrophysics Data System (ADS)

    Gao, Yuan; Liu, Jian-Guo; Lu, Jianfeng

    2016-12-01

    This work considers the rigorous derivation of continuum models of step motion starting from a mesoscopic Burton-Cabrera-Frank-type model following the Xiang's work (Xiang in SIAM J Appl Math 63(1):241-258, 2002). We prove that as the lattice parameter goes to zero, for a finite time interval, a modified discrete model converges to the strong solution of the limiting PDE with first-order convergence rate.

  4. Mesoscopic tomography imaging of reporter genes in thick printed tissue constructs

    NASA Astrophysics Data System (ADS)

    Ozturk, Mehmet S.; Lee, Vivian K.; Zhao, Lingling; Dai, Guohoa; Intes, Xavier

    2013-06-01

    We report an application of Mesoscopic Fluorescence Molecular Tomography to 3D tissue engineering construct. Engineered thick tissue was hosting two 3D printed vasculatures. The channels were formed by live cells, expressing GFP and mCherry reporter genes, embedded in 3mm turbid media. Tissue and cells kept in a 3mm thick perfusion chamber during the entire imaging process which took less than 5 minutes.

  5. Continuum Limit of a Mesoscopic Model with Elasticity of Step Motion on Vicinal Surfaces

    NASA Astrophysics Data System (ADS)

    Gao, Yuan; Liu, Jian-Guo; Lu, Jianfeng

    2017-06-01

    This work considers the rigorous derivation of continuum models of step motion starting from a mesoscopic Burton-Cabrera-Frank-type model following the Xiang's work (Xiang in SIAM J Appl Math 63(1):241-258, 2002). We prove that as the lattice parameter goes to zero, for a finite time interval, a modified discrete model converges to the strong solution of the limiting PDE with first-order convergence rate.

  6. Microstructural Evolution and Irreversibility in the Viscoelastic Response of Mesoscopic Dusty-Plasma Liquids

    SciTech Connect

    Chan, C.-L.; I, L.

    2007-03-09

    We experimentally demonstrate the viscoelastic response and construct a microscopic dynamical picture using a quasi-2D dusty-plasma liquid confined in a mesoscopic gap and sheared periodically. The correlation between microdisplacement and structural evolution at the discrete kinetic level is explored. Through hopping, the structural rearrangement associated with shear enhanced stretching, kinking, breaking, and reconnection of local lattice lines generates irreversible plastic deformation. The strain energy accumulation in the twisted regions without topological rearrangement is the source for local rebound.

  7. Mesoscopic competition of superconductivity and ferromagnetism: conductance peak statistics for metallic grains.

    PubMed

    Schmidt, S; Alhassid, Y

    2008-11-14

    We investigate the competition between superconductivity and ferromagnetism in chaotic ultrasmall metallic grains in a regime where both phases can coexist. We use an effective Hamiltonian that combines a BCS-like pairing term and a ferromagnetic Stoner-like spin exchange term. We study the transport properties of the grain in the Coulomb-blockade regime and identify signatures of the coexistence of pairing and exchange correlations in the mesoscopic fluctuations of the conductance peak spacings and peak heights.

  8. Numerical Simulation of Mesoscopic Systems with Open Boundaries Using the Multidimensional Time-Dependent Schroedinger Equation

    DTIC Science & Technology

    1991-05-15

    dependent Schr ~ dinger equation , and a Dis~tribut ion/ numrerical implementation of absorbing boundary conditions for propagating wavefunctions atf the...mesoscopic systems with open boundaries using the multidirnensiji.j* time - dependent Schrodinger equation 12. PERSONAL AUTHOR(S) Register, Leonard F...if necessary and identify by block number) A numerical procedure based on the time - dependent Schroainger equation for the modelin~g of multidimensional

  9. A method for biological testing of containment systems for viral agents.

    PubMed

    Bolton, N E; Lincoln, T A; Otten, J A; Porter, W E

    1976-07-01

    A technique utilizing coliphage as the test material has been developed and employed to evaluate the effectiveness of a containment system for zonal centrifugation of hepatits viruses. An Andersen Viable Particle Sampler which had been loaded with plates containing a base layer of agar nutrient with an overlay of E. coli- agar suspension was used to sample the test air. The containment system, which includes a HEPA filter, was challenged with an aerosolized suspension of coliphage.

  10. Investigation and field testing of anaerobic biological treatment of pharmaceutical wastewaters

    SciTech Connect

    Not Available

    1990-03-30

    A study has been conducted that investigated and demonstrated the anaerobic biological treatment of wastewaters generated by the pharmaceuticals industry. This report presents the results of the multi-phase program and the conclusions and recommendations which have been derived from an analysis of the experimental data. The program was initiated in October 1985 and was conducted over a period of 26 months, at which point the experimental portions of the study were completed in December 1987. These can be divided to essentially three major tasks: screening assays to assess anaerobic treatability; bench-scale treatability investigations of the Merck Stonewall Plant wastewaters; and, pilot scale demonstration of anaerobic treatment. Each major element is discussed separately, addressing the design of the program (facilities), the experimental procedures, and finally the results of each task. The final section discusses the application of the technology to the pharmaceutical industry and the economic components associated with it. 2 refs., 54 figs., 35 tabs.

  11. Mesoscopic Interactions and Species Coexistence in Evolutionary Game Dynamics of Cyclic Competitions

    NASA Astrophysics Data System (ADS)

    Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

    2014-12-01

    Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

  12. Mesoscopic CH3NH3PbI3/TiO2 heterojunction solar cells.

    PubMed

    Etgar, Lioz; Gao, Peng; Xue, Zhaosheng; Peng, Qin; Chandiran, Aravind Kumar; Liu, Bin; Nazeeruddin, Md K; Grätzel, Michael

    2012-10-24

    We report for the first time on a hole conductor-free mesoscopic methylammonium lead iodide (CH(3)NH(3)PbI(3)) perovskite/TiO(2) heterojunction solar cell, produced by deposition of perovskite nanoparticles from a solution of CH(3)NH(3)I and PbI(2) in γ-butyrolactone on a 400 nm thick film of TiO(2) (anatase) nanosheets exposing (001) facets. A gold film was evaporated on top of the CH(3)NH(3)PbI(3) as a back contact. Importantly, the CH(3)NH(3)PbI(3) nanoparticles assume here simultaneously the roles of both light harvester and hole conductor, rendering superfluous the use of an additional hole transporting material. The simple mesoscopic CH(3)NH(3)PbI(3)/TiO(2) heterojunction solar cell shows impressive photovoltaic performance, with short-circuit photocurrent J(sc)= 16.1 mA/cm(2), open-circuit photovoltage V(oc) = 0.631 V, and a fill factor FF = 0.57, corresponding to a light to electric power conversion efficiency (PCE) of 5.5% under standard AM 1.5 solar light of 1000 W/m(2) intensity. At a lower light intensity of 100W/m(2), a PCE of 7.3% was measured. The advent of such simple solution-processed mesoscopic heterojunction solar cells paves the way to realize low-cost, high-efficiency solar cells.

  13. Mesoscopic Framework Enables Facile Ionic Transport in Solid Electrolytes for Li Batteries

    DOE PAGES

    Ma, Cheng; Cheng, Yongqiang; Chen, Kai; ...

    2016-03-29

    In Li-ion-conducting solid electrolytes can simultaneously overcome two grand challenges for Li-ion batteries: the severe safety concerns that limit the large-scale application and the poor electrolyte stability that forbids the use of high-voltage cathodes. Nevertheless, the ionic conductivity of solid electrolytes is typically low, compromising the battery performances. Precisely determining the ionic transport mechanism(s) is a prerequisite for the rational design of highly conductive solid electrolytes. For decades, the research on this subject has primarily focused on the atomic and microscopic scales, where the main features of interest are unit cells and microstructures, respectively. We show that the largely overlookedmore » mesoscopic scale lying between these extremes could be the key to fast ionic conduction. In a prototype system, (Li0.33La0.56)TiO3, a mesoscopic framework is revealed for the first time by state-of-the-art scanning transmission electron microscopy. Corroborated by theoretical calculations and impedance measurements, it is demonstrated that such a unique configuration maximizes the number of percolation directions and thus most effectively improves the ionic conductivity. Finally, this discovery reconciles the long-standing structure–property inconsistency in (Li0.33La0.56)TiO3 and also identifies mesoscopic ordering as a promising general strategy for optimizing Li+ conduction.« less

  14. Mesoscopic Framework Enables Facile Ionic Transport in Solid Electrolytes for Li Batteries

    SciTech Connect

    Ma, Cheng; Cheng, Yongqiang; Chen, Kai; Li, Juchuan; Sumpter, Bobby G.; Nan, Ce-Wen; More, Karren L.; Dudney, Nancy J.; Chi, Miaofang

    2016-03-29

    In Li-ion-conducting solid electrolytes can simultaneously overcome two grand challenges for Li-ion batteries: the severe safety concerns that limit the large-scale application and the poor electrolyte stability that forbids the use of high-voltage cathodes. Nevertheless, the ionic conductivity of solid electrolytes is typically low, compromising the battery performances. Precisely determining the ionic transport mechanism(s) is a prerequisite for the rational design of highly conductive solid electrolytes. For decades, the research on this subject has primarily focused on the atomic and microscopic scales, where the main features of interest are unit cells and microstructures, respectively. We show that the largely overlooked mesoscopic scale lying between these extremes could be the key to fast ionic conduction. In a prototype system, (Li0.33La0.56)TiO3, a mesoscopic framework is revealed for the first time by state-of-the-art scanning transmission electron microscopy. Corroborated by theoretical calculations and impedance measurements, it is demonstrated that such a unique configuration maximizes the number of percolation directions and thus most effectively improves the ionic conductivity. Finally, this discovery reconciles the long-standing structure–property inconsistency in (Li0.33La0.56)TiO3 and also identifies mesoscopic ordering as a promising general strategy for optimizing Li+ conduction.

  15. Mesoscopic Interactions and Species Coexistence in Evolutionary Game Dynamics of Cyclic Competitions

    PubMed Central

    Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

    2014-01-01

    Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species. PMID:25501627

  16. Primary thermometry triad at 6 mK in mesoscopic circuits

    PubMed Central

    Iftikhar, Z.; Anthore, A.; Jezouin, S.; Parmentier, F. D.; Jin, Y.; Cavanna, A.; Ouerghi, A.; Gennser, U.; Pierre, F.

    2016-01-01

    Quantum physics emerge and develop as temperature is reduced. Although mesoscopic electrical circuits constitute an outstanding platform to explore quantum behaviour, the challenge in cooling the electrons impedes their potential. The strong coupling of such micrometre-scale devices with the measurement lines, combined with the weak coupling to the substrate, makes them extremely difficult to thermalize below 10 mK and imposes in situ thermometers. Here we demonstrate electronic quantum transport at 6 mK in micrometre-scale mesoscopic circuits. The thermometry methods are established by the comparison of three in situ primary thermometers, each involving a different underlying physics. The employed combination of quantum shot noise, quantum back action of a resistive circuit and conductance oscillations of a single-electron transistor covers a remarkably broad spectrum of mesoscopic phenomena. The experiment, performed in vacuum using a standard cryogen-free dilution refrigerator, paves the way towards the sub-millikelvin range with additional thermalization and refrigeration techniques. PMID:27659941

  17. Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations

    NASA Astrophysics Data System (ADS)

    Flegg, Mark B.; Hellander, Stefan; Erban, Radek

    2015-05-01

    In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: Δt → 0 and h is fixed; Δt → 0 and h → 0 such that √{ Δt } / h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.

  18. Combining molecular dynamics with mesoscopic Green’s function reaction dynamics simulations

    SciTech Connect

    Vijaykumar, Adithya; Bolhuis, Peter G.; Rein ten Wolde, Pieter

    2015-12-07

    In many reaction-diffusion processes, ranging from biochemical networks, catalysis, to complex self-assembly, the spatial distribution of the reactants and the stochastic character of their interactions are crucial for the macroscopic behavior. The recently developed mesoscopic Green’s Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. We propose a novel approach that combines GFRD for simulating the system at the mesoscopic scale where particles are far apart, with a microscopic technique such as Langevin dynamics or Molecular Dynamics (MD), for simulating the system at the microscopic scale where reactants are in close proximity. This scheme defines the regions where the particles are close together and simulated with high microscopic resolution and those where they are far apart and simulated with lower mesoscopic resolution, adaptively on the fly. The new multi-scale scheme, called MD-GFRD, is generic and can be used to efficiently simulate reaction-diffusion systems at the particle level.

  19. Mesoscopic behaviour of multi-layered graphene: the meaning of supercapacitance revisited.

    PubMed

    Gutierrez, Fabiana A; Bedatty Fernandes, Flavio C; Rivas, Gustavo A; Bueno, Paulo R

    2017-03-01

    The electronic density of states and its contribution to the capacitance of graphene compounds (oxidized and reduced) were investigated using an electrochemical impedance-derived capacitance spectroscopic approach. It is clearly demonstrated that graphene oxide, which is known to exhibit semiconductor electronic characteristics, has little influence on the magnitude of the measured capacitance. Moreover, when graphene oxide is electrochemically reduced to graphene, the capacitance increases dramatically by about three orders of magnitude (from microfaradays to millifaradays). This increased capacitive effect has been interpreted as being directly associated with the electrochemical non-faradaic (super- or ultracapacitive) characteristics of the interface (i.e. associated with its electroactive area, for instance). The results obtained and interpretation made in this work demonstrate that the magnitude of the measured capacitance is a consequence of an electrochemical capacitive phenomenon (mesoscopic in essence; thus, the associated capacitance is equivalently termed mesoscopic capacitance) that energetically contains, in series, both electrostatic (geometrical) and quantum effects, thus being essentially different from those exclusively related to the amount of existing interfacial sites for ions (i.e. beyond those associated with pure double-layer capacitive effects). Conceptually, it is proposed that the mesoscopic capacitance of reduced graphene can be explained mainly through quantum chemical effects, ultimately following first-principles quantum mechanics supported on density functional theory, wherein the density of states is central.

  20. Mesoscopic interactions and species coexistence in evolutionary game dynamics of cyclic competitions.

    PubMed

    Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

    2014-12-15

    Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

  1. Biological and analytical variations of 16 parameters related to coagulation screening tests and the activity of coagulation factors.

    PubMed

    Chen, Qian; Shou, Weiling; Wu, Wei; Guo, Ye; Zhang, Yujuan; Huang, Chunmei; Cui, Wei

    2015-04-01

    To accurately estimate longitudinal changes in individuals, it is important to take into consideration the biological variability of the measurement. The few studies available on the biological variations of coagulation parameters are mostly outdated. We confirmed the published results using modern, fully automated methods. Furthermore, we added data for additional coagulation parameters. At 8:00 am, 12:00 pm, and 4:00 pm on days 1, 3, and 5, venous blood was collected from 31 healthy volunteers. A total of 16 parameters related to coagulation screening tests as well as the activity of coagulation factors were analyzed; these included prothrombin time, fibrinogen (Fbg), activated partial thromboplastin time, thrombin time, international normalized ratio, prothrombin time activity, activated partial thromboplastin time ratio, fibrin(-ogen) degradation products, as well as the activity of factor II, factor V, factor VII, factor VIII, factor IX, and factor X. All intraindividual coefficients of variation (CVI) values for the parameters of the screening tests (except Fbg) were less than 5%. Conversely, the CVI values for the activity of coagulation factors were all greater than 5%. In addition, we calculated the reference change value to determine whether a significant difference exists between two test results from the same individual.

  2. Ecological evaluation of proposed dredged material from the John F. Baldwin Ship Channel: Phase 3 -- biological testing

    SciTech Connect

    Kohn, N.P.; Karle, L.M.; Pinza, M.R.; Mayhew, H.L.; White, P.J.; Gruendell, B.D.; Word, J.Q.

    1993-10-01

    The John F. Baldwin Ship Channel is a 28-mile-long portion of the San Francisco Bay to Stockton Ship Channel, the primary shipping lane through San Francisco Bay and Delta. The San Francisco District of the US Army Corps of Engineers (USACE) is responsible for construction of the John F. Baldwin Ship Channel, which is authorized to be deepened to a project depth of {minus}45 ft relative to mean lower low water (MLLW). Approximately 8.5 million cubic yards (mcy) of sediment will be removed from the channel to reach this project depth. The USACE requested Battelle/Marine Sciences Laboratory (MSL) to conduct testing for ocean disposal under the guidelines in Evaluation of Dredged Material Proposed for Ocean Disposal-Testing Manual (EPA/USACE 1991). This testing manual contains a tiered evaluation approach developed specifically for ocean disposal of dredged material at a selected site. In this study, John F. Baldwin Ship Channel sediments were evaluated under the Tier III (biological) testing guidance, which is considered to be highly stringent and protective of the environment. The Tier III guidance for ocean disposal testing requires tests of water column effects, (following dredged material disposal), deposited sediment toxicity, and bioaccumulation of contaminants from deposited sediment (dredged material).

  3. Surfzone Bubbles: Model Development, Testing and Extension to Sedimentary/Chemical/Biological Processes

    DTIC Science & Technology

    2013-09-30

    inundation", Ocean Modelling, 43-44, 36-51. Shi, F., Kirby, J . T., Ma, G., Holman , R. A. and Chickadel, C. C., 2012b, "Field testing model predictions...Shi, F., Kirby, J . T., Ma, G., Holman , R. A. and Chickadel, C. C., 2012b, "Field testing model predictions of foam coverage and bubble content...outflows and their effects on the delivery and resuspension of sediments in the near field. REFERENCES Blenkinsopp, C. E. and Chaplin, J . R., 2007

  4. Development and testing of new biologically-based polymers as advanced biocompatible contact lenses

    SciTech Connect

    Bertozzi, Carolyn R.

    2000-06-01

    Nature has evolved complex and elegant materials well suited to fulfill a myriad of functions. Lubricants, structural scaffolds and protective sheaths can all be found in nature, and these provide a rich source of inspiration for the rational design of materials for biomedical applications. Many biological materials are based in some fashion on hydrogels, the crosslinked polymers that absorb and hold water. Biological hydrogels contribute to processes as diverse as mineral nucleation during bone growth and protection and hydration of the cell surface. The carbohydrate layer that coats all living cells, often referred to as the glycocalyx, has hydrogel-like properties that keep cell surfaces well hydrated, segregated from neighboring cells, and resistant to non-specific protein deposition. With the molecular details of cell surface carbohydrates now in hand, adaptation of these structural motifs to synthetic materials is an appealing strategy for improving biocompatibility. The goal of this collaborative project between Prof. Bertozzi's research group, the Center for Advanced Materials at Lawrence Berkeley National Laboratory and Sunsoft Corporation was the design, synthesis and characterization of novel hydrogel polymers for improved soft contact lens materials. Our efforts were motivated by the urgent need for improved materials that allow extended wear, and essential feature for those whose occupation requires the use of contact lenses rather than traditional spectacles. Our strategy was to transplant the chemical features of cell surface molecules into contact lens materials so that they more closely resemble the tissue in which they reside. Specifically, we integrated carbohydrate molecules similar to those found on cell surfaces, and sulfoxide materials inspired by the properties of the carbohydrates, into hydrogels composed of biocompatible and manufacturable substrates. The new materials were characterized with respect to surface and bulk hydrophilicity, and

  5. 40 CFR 230.61 - Chemical, biological, and physical evaluation and testing.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... potential effects on the water column and on communities of aquatic organisms. (1) Evaluation of chemical... in § 230.60, that the likelihood of contamination by contaminants is acceptably low, unless the... be obtained from bioassays in lieu of chemical tests. (2) Water column effects. (i)...

  6. Stress test of a biological early warning system with zebrafish (Danio rerio).

    PubMed

    Amorim, João; Fernandes, Miguel; Vasconcelos, Vitor; Oliva Teles, Luis

    2017-01-01

    The aim of this work was to develop a novel methodology to stress test the diagnostic capability of a video tracking system with zebrafish (Danio rerio), against two pre-established disturbances. Eight different treatments were tested varying the presence or absence of a toxicant (NaOCl) and two disturbances: the passing of a shadow (mimicking a predator) and entrapment of the fish. The concentration tested corresponded to a sublethal (1 % 24 h-LC50) and short term exposure (2 h). A total of 56 organisms were tested resulting in 112 diagnoses (before and after the contamination). A statistical model of diagnosis was developed using Self-organizing Map (SOM) and Correspondence Analysis (CA). Sensitivity, specificity, accuracy, false positive and false negative values were calculated to evaluate the diagnostic performance. The disturbances did not negatively affect the capability of the model. In the presence of at least one of these variables, the diagnostic performance was similar or even superior to the baseline results without disturbances. Furthermore, the system produced a large number of correct diagnoses, at an ecologically relevant concentration of exposure, in a non-invasive way.

  7. 77 FR 26162 - Amendments to Sterility Test Requirements for Biological Products

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-03

    ... HUMAN SERVICES Food and Drug Administration 21 CFR Parts 600, 610, and 680 Amendments to Sterility Test... apply to Whole Blood, Cryoprecipitated Antihemophilic Factor (AHF), Platelets, Red Blood Cells, Plasma, Source Plasma, Smallpox Vaccine, Reagent Red Blood Cells, Anti-Human Globulin, or Blood Grouping Reagents...

  8. Testing sediment biological effects with the freshwater amphipod Hyalella azteca: the gap between laboratory and nature.

    PubMed

    Wang, Feiyue; Goulet, Richard R; Chapman, Peter M

    2004-12-01

    The freshwater amphipod, Hyalella azteca, is widely used in laboratory sediment toxicity and bioaccumulation tests. However, its responses in the laboratory are probably very different from those in the field. A review of the literature indicates that in its natural habitat this species complex is primarily epibenthic, derives little nutrition from the sediments, and responds primarily to contaminants in the overlying water column (including water and food), not sediment or porewater. In laboratory sediment toxicity tests H. azteca is deprived of natural food sources such as algal communities on or above the sediments, and is subjected to constant light without any cover except that afforded by burial into the sediments. Under these constraining laboratory conditions, H. azteca has been reported to respond to sediment or porewater contamination. In nature, contamination of overlying water from sediment is less likely than in the laboratory because of the large, generally non-static sink of natural surface water. H. azteca does not appear to be the most appropriate test species for direct assessments of the bioavailability and toxicity of sediment contaminants, though it is probably appropriate for testing the toxicity of surface waters. Toxic and non-toxic responses will be highly conservative, though the latter are probably the most persuasive given the exposure constraints. Thus H. azteca is probably a suitable surrogate species for determining sediments that are likely not toxic to field populations; however, it is not suitable for determining sediments that are likely toxic to field populations.

  9. [Determination of tumor biological parameters in breast cancer: round robin testing for quality assurance].

    PubMed

    Liessem, S; Winkens, W; Jonigk, D; Wasielewski, R V; Fisseler-Eckhoff, A; Rüschoff, J; Kreipe, H-H

    2014-02-01

    Round robin testing for quality assurance in the determination of the breast cancer biomarkers estrogen receptor (ER), progesterone receptor (PR) and epithelial growth factor receptor 2 (HER2) have been carried out in Germany for 13 years. As the first quality assurance trial worldwide tissue microarrays with 20 different breast cancer specimens were used. As a further innovation the challenges were split into a test part representing routine cases and a training part enriched with difficult borderline cases in order to uncover latent weaknesses in the participating laboratories. Certificates are issued based exclusively on the test part. Similar to NordiQC and UKNequas stained slides are assessed externally and the quality of staining and evaluation are considered separately. Since 2010 an additional internet-based trial without assessment of the staining quality is offered for ER and PR. Since the introduction of the round robin trials the numbers of participants (n = 200-250) and the success rates have steadily increased. The breast cancer quality assurance trial ranks first with regard to the number of participants in Germany. It could be demonstrated that regular participation in the round robin test leads to an improvement of staining results of ER, PR and HER2 and hence appears to be mandatory for maintaining quality standards. The use of fully automated immunohistochemical staining procedures has steadily increased and these are now used by approximately 50 % of participants.

  10. 77 FR 22282 - Draft Guidelines on Biologics Quality Monitoring: Testing for the Detection of Mycoplasma...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-13

    ... master seed/cell testing in veterinary vaccines regulated by the Animal and Plant Health Inspection... products through the master seeds, the master cell seed (stock), starting materials of animal origin, and... seed, master cell seed, and ingredients of animal origin. The draft guideline establishes stages of...

  11. Some biological aspects of Mysidopsis juniae (Crustacea:Mysidacea) and its use in chronic toxicity tests

    SciTech Connect

    Badaro-Pedroso, C. Nipper, M.G.

    1995-12-31

    As part of the joint effort to develop marine toxicity tests with organisms abundant at the Brazilian coast, some aspects for the laboratory culture of M. juniae and its sensitivity to single chemicals were studied. Organisms fed a mixture of brine shrimp (Artemia sp.) nauplii and the microalgae Isochrysis galbana reached sexual maturity 10 days before animals fed brine shrimp nauplii only. Under best conditions, sexual maturity was reached on the 9th--11th day and newborn mysids hatched on the 16th--18th day, Short-term chronic toxicity tests were initiated with 7-day old mysids and exposure time was 11 days, with growth (length and dry weight) as test endpoints. Experiments were undertaken with zinc, copper, and ammonia. Zinc did not affect the organisms at concentrations between 0.018 and 0.1 mg/L, which were one order of magnitude lower than the average 96-h; LC50 value. The NOEC and LOEC values were the same for length and weight in some tests with copper and ammonia (Cu: 0.006 and 0.015 mg/L; NH{sub 3}: 0.32 and 0.87 mg/L, respectively), but revealed length as a more sensitive endpoint than weight in others (length NOEC and LOEC: 0.23 and 0.53 mgNH{sub 3}/L; weight: 0.53 and 0.99 mgNH{sub 3}/L, respectively). The authors speculate that this could be caused by time-dependent variations in the lipid content of the organisms. Length would be a steadier and more reliable endpoint for chronic toxicity tests with M. juniae. The results show that the method has potential applications for the evaluation and monitoring of contaminated marine systems along the Brazilian coast.

  12. Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks.

    PubMed

    Newberry, Mitchell G; Ennis, Daniel B; Savage, Van M

    2015-08-01

    Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to capillaries and uses scaling exponents to quantify these changes. Prominent scaling theories predict that combinations of these exponents explain how metabolic, growth, and other biological rates vary with body size. Nevertheless, direct measurements of individual vessel segments have been limited because existing techniques for measuring vasculature are invasive, time consuming, and technically difficult. We developed software that extracts the length, radius, and connectivity of in vivo vessels from contrast-enhanced 3D Magnetic Resonance Angiography. Using data from 20 human subjects, we calculated scaling exponents by four methods-two derived from local properties of branching junctions and two from whole-network properties. Although these methods are often used interchangeably in the literature, we do not find general agreement between these methods, particularly for vessel lengths. Measurements for length of vessels also diverge from theoretical values, but those for radius show stronger agreement. Our results demonstrate that vascular network models cannot ignore certain complexities of real vascular systems and indicate the need to discover new principles regarding vessel lengths.

  13. Biological process design and pilot testing for a carbon oxidation, nitrification, and denitrification system

    SciTech Connect

    Givens, S.W.; Brown, E.V. ); Gelman, S.R. ); Grady, C.P.L. Jr. ); Skedsvold, D.A. )

    1991-05-01

    In response to a new NPDES permit incorporating Organic Chemical, Plastic, and Synthetic Fiber (OCPSF) effluent limits for BOD (carbonaceous and nitrogenous), TSS, and priority pollutants, a treatability study was conducted to establish design criteria for a new process wastewater treatment plant for DSM Chemicals North America, Inc. The permit also requires partial removal of total nitrogen. Based on the discharge criteria, a two-stage biological process configuration was selected. The configuration consisted of an anoxic followed by an aerobic reactor with mixed liquor recirculation. To establish design criteria, a two-phase study was conducted. The first phase involved determining wastewater characteristics and kinetic and stoichiometric coefficients. These values were used as input to Simulation of Single-Sludge Processes (SSSP), a computer model that was used to evaluate potential process configurations. In the second phase, a pilot-scale system was operated to verify performance. With a volume distribution of 40% anoxic and 60% aerobic and recirculation ratio of 2, BOD, COD, and total nitrogen removal efficiencies of 99, 88, and 80% were obtained, respectively. Approximately 84% of the biodegradable COD was removed through denitrification.

  14. The Acid Test for Biological Science: STAP Cells, Trust, and Replication.

    PubMed

    Lancaster, Cheryl

    2016-02-01

    In January 2014, a letter and original research article were published in Nature describing a process whereby somatic mouse cells could be converted into stem cells by subjecting them to stress. These "stimulus-triggered acquisition of pluripotency" (STAP) cells were shown to be capable of contributing to all cell types of a developing embryo, and extra-embryonic tissues. The lead author of the publications, Haruko Obokata, became an overnight celebrity in Japan, where she was dubbed the new face of Japanese science. However, in the weeks that followed publication of the research, issues arose. Other laboratories and researchers (including authors on the original papers) found that they were unable to replicate Obokata et al.'s work. Closer scrutiny of the papers by the scientific community also suggested that there was manipulation of images that had been published, and Obokata was accused of misconduct. Those who should have been supervising her work (also her co-authors on the publications) were also heavily criticised. The STAP cell saga of 2014 is used as an example to highlight the importance of trust and replication in twenty-first century biological science. The role of trust in the scientific community is highlighted, and the effects on interactions between science and the public examined. Similarly, this essay aims to highlight the importance of replication, and how this is understood by researchers, the media, and the public. The expected behaviour of scientists in the twenty-first century is now more closely scrutinised.

  15. 1994 Baseline biological studies for the Device Assembly Facility at the Nevada Test Site

    SciTech Connect

    Townsend, Y.E.; Woodward, B.D.; Hunter, R.B.; Greger, P.D.; Saethre, M.B.

    1995-02-01

    This report describes environmental work performed at the Device Assembly Facility (DAF) in 1994 by the Basic Environmental Monitoring and Compliance Program (BECAMP). The DAF is located near the Mojave-Great Basin desert transition zone 27 km north of Mercury. The area immediately around the DAF building complex is a gentle slope cut by 1 to 3 m deep arroyos, and occupied by transitional vegetation. In 1994, construction activities were largely limited to work inside the perimeter fence. The DAF was still in a preoperational mode in 1994, and no nuclear materials were present. The DAF facilities were being occupied so there was water in the sewage settling pond, and the roads and lights were in use. Sampling activities in 1994 represent the first year in the proposed monitoring scheme. The proposed biological monitoring plan gives detailed experimental protocols. Plant, lizard, tortoise, small mammal, and bird surveys were performed in 1994. The authors briefly outline procedures employed in 1994. Studies performed on each taxon are reviewed separately then summarized in a concluding section.

  16. Dissolution testing and potentiometric determination of famciclovir in pure, dosage forms and biological fluids.

    PubMed

    Rezk, Mohamed S; El Nashar, Rasha M

    2013-02-01

    The performance characteristics of two new plastic membrane ion selective electrodes (ISEs) used for the determination of famciclovir (Fcv) based on the ion associate of Fcv with phosphotungstic acid (PTA) or phosphomolybdic acid (PMA) are described. Different experimental conditions as type of plasticizer to be incorporated in the membrane, life span, effect of soaking, pH, temperature, and interferences were studied. Both electrodes showed similar performance under these conditions, exhibiting Nernstian slopes of S (Fcv-PTA)=58.60±0.84 mV/decade and S (Fcv-PMA)=58.77±0.68 mV/decade within a usable concentration range of 10⁻⁵-10⁻² [Fcv/M] at 298/K. Famciclovir was assayed potentiometrically in its pure solution, pharmaceutical preparations and biological fluids (urine and plasma) using proposed electrodes under batch and flow injection analysis (FIA) conditions with a recovery % ranging between 96.76% and 102.83% having RSD of 0.66%-1.81%. The electrodes were also successfully applied in the determination of the dissolution profile of Fcv tablets and the results came in agreement with the validated results of the HPLC method obtained from the quality control unit of the company producing the tablets.

  17. The most informative spacing test effectively discovers biologically relevant outliers or multiple modes in expression

    PubMed Central

    Wu, Gang; Edmonson, Michael; Liu, Zhifa; Gruber, Tanja; Zhang, Jinghui; Pounds, Stan

    2014-01-01

    Summary: Several outlier and subgroup identification statistics (OASIS) have been proposed to discover transcriptomic features with outliers or multiple modes in expression that are indicative of distinct biological processes or subgroups. Here, we borrow ideas from the OASIS methods in the bioinformatics and statistics literature to develop the ‘most informative spacing test’ (MIST) for unsupervised detection of such transcriptomic features. In an example application involving 14 cases of pediatric acute megakaryoblastic leukemia, MIST more robustly identified features that perfectly discriminate subjects according to gender or the presence of a prognostically relevant fusion-gene than did seven other OASIS methods in the analysis of RNA-seq exon expression, RNA-seq exon junction expression and micorarray exon expression data. MIST was also effective at identifying features related to gender or molecular subtype in an example application involving 157 adult cases of acute myeloid leukemia. Availability: MIST will be freely available in the OASIS R package at http://www.stjuderesearch.org/site/depts/biostats Contact: stanley.pounds@stjude.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24458951

  18. Engineering aspects of the experiment and results of animal tests. [Apollo 17 Biological Cosmic Ray Experiment

    NASA Technical Reports Server (NTRS)

    Look, B. C.; Tremor, J. W.; Barrows, W. F.; Zabower, H. R.; Suri, K.; Park, E. G., Jr.; Durso, J. A.; Leon, H. A.; Haymaker, W.; Lindberg, R. G.

    1975-01-01

    A closed passive system independent of support from the spacecraft or its crew was developed to house five pocket mice for their flight on Apollo XVII. The reaction of potassium superoxide with carbon dioxide and water vapor to produce oxygen provided a habitable atmosphere within the experiment package. The performance of the system and the ability of the mice to survive the key preflight tests gave reasonable assurance that the mice would also withstand the Apollo flight.-

  19. ``Test kit'' for detection of biologically important anions: A salicylidene-hydrazine based Schiff base

    NASA Astrophysics Data System (ADS)

    Dalapati, Sasanka; Alam, Md Akhtarul; Jana, Sankar; Karmakar, Saswati; Guchhait, Nikhil

    2013-02-01

    Test paper coated with Schiff base [(N,N/-bis(5-nitro-salicylidene)hydrazine] receptor 1 (host) can selectively detect fluoride and acetate ions (guest) by developing yellow color which can be detected by naked-eye both in aqueous-acetonitrile solution and in solid supported test kit. UV-vis spectral analysis shows that the absorption peaks at 288 and 345 nm of receptor 1 gradually decrease its initial intensity and new red shifted absorption bands at 397 nm and 455 nm gradually appear upon addition of increasing amount of F- and AcO- ions over several tested anions such as HPO4-, Cl, Br, I, NO3-, NO2-, HSO4-, HSO3-, and ClO4- in aqueous-acetonitrile solvent. The colorimetric test results and UV-vis spectral analysis are in well agreement with 1H NMR titration results in d6-DMSO solvent. The receptor 1 forms 1:2 stable complexes with F- and AcO- ions. However, similar kind of observation obtained from UV-vis titrations in presence of AcOH corresponds to 1:1 complexation ratio indicating the formation of H-bonding interaction between the receptor and anions (F- and AcO- ions). So, the observed 1:2 complexation ratio can only be explained on the basis of deprotonation (˜1 eqv.) and H-bonding (˜1 eqv.) interactions [1]. The ratiometric analysis of host-guest complexes corroborates well with the proposed theoretical model optimization at Density Functional Theory (DFT) level.

  20. Engineering aspects of the experiment and results of animal tests. [Apollo 17 Biological Cosmic Ray Experiment

    NASA Technical Reports Server (NTRS)

    Look, B. C.; Tremor, J. W.; Barrows, W. F.; Zabower, H. R.; Suri, K.; Park, E. G., Jr.; Durso, J. A.; Leon, H. A.; Haymaker, W.; Lindberg, R. G.

    1975-01-01

    A closed passive system independent of support from the spacecraft or its crew was developed to house five pocket mice for their flight on Apollo XVII. The reaction of potassium superoxide with carbon dioxide and water vapor to produce oxygen provided a habitable atmosphere within the experiment package. The performance of the system and the ability of the mice to survive the key preflight tests gave reasonable assurance that the mice would also withstand the Apollo flight.-

  1. "Test kit" for detection of biologically important anions: a salicylidene-hydrazine based Schiff base.

    PubMed

    Dalapati, Sasanka; Alam, Md Akhtarul; Jana, Sankar; Karmakar, Saswati; Guchhait, Nikhil

    2013-02-01

    Test paper coated with Schiff base [(N,N(/)-bis(5-nitro-salicylidene)hydrazine] receptor 1 (host) can selectively detect fluoride and acetate ions (guest) by developing yellow color which can be detected by naked-eye both in aqueous-acetonitrile solution and in solid supported test kit. UV-vis spectral analysis shows that the absorption peaks at 288 and 345 nm of receptor 1 gradually decrease its initial intensity and new red shifted absorption bands at 397 nm and 455 nm gradually appear upon addition of increasing amount of F(-) and AcO(-) ions over several tested anions such as H(2)PO(4)(-), Cl(-), Br(-), I(-), NO(3)(-), NO(2)(-), HSO(4)(-), HSO(3)(-), and ClO(4)(-) in aqueous-acetonitrile solvent. The colorimetric test results and UV-vis spectral analysis are in well agreement with (1)H NMR titration results in d(6)-DMSO solvent. The receptor 1 forms 1:2 stable complexes with F(-) and AcO(-) ions. However, similar kind of observation obtained from UV-vis titrations in presence of AcOH corresponds to 1:1 complexation ratio indicating the formation of H-bonding interaction between the receptor and anions (F(-) and AcO(-) ions). So, the observed 1:2 complexation ratio can only be explained on the basis of deprotonation (∼1 eqv.) and H-bonding (∼1 eqv.) interactions [1]. The ratiometric analysis of host-guest complexes corroborates well with the proposed theoretical model optimization at Density Functional Theory (DFT) level.

  2. Evaluation of some biological tests as parameters for microbial activities in soils. II. Field investigations.

    PubMed

    Abd-El-Malek, Y; Monib, M; Rizk, S G; Shehata, S M

    1976-01-01

    Investigations were designed to study the effect of certain factors on the microbial activities in soil. The parameters, used as an index of the microbial activities, were total bacterial counts, dehydrogenase activity, oxidation of organic carbon, and CO2 evolved/7 days. Bahteem Farm clay soil was examined for determining the effects of depth, type of fertilization, and crop rotation on the microbial activities. It appears that the microbial activities, as indicated by the tested parameters, were more pronounced in the surface 15 cm-layer than in the subsurface layer (15-30 cm). Results of all the parameters tested showed markedly higher increases with farmyard manure than with nitrogenous fertilizer and in the control, without significant differences between the latter two. Moreover, the time of sampling had no effect on the results obtained for all parameters. Different types of rotations did not exert significant variation in total bacterial counts, though more than one crop per year increased the organic carbon content of soil and mostly the dehydrogenase activity, whereas the evolution of CO2 tended to decrease. At Gabal el-Asfar Farm, the effect of irrigation with sewage effluent, for long periods, on the microbial activities of sandy soil was investigated. Sewage water stimulated the total bacteria, raised the dehydrogenase activity, the organic carbon, and the production of CO2. In North El Tahreer and Mariut Sectors, the effect of both the type and age of cultivation on the microbial activities in the calcareous soils were examined. Cultivation raised the figures of all the tested parameters progressively with time of cultivation. It was also noticed that crops exerted more beneficial effects on microbial activities than orchards, and the dehydrogenase test was the most reliable parameter to reveal this fact.

  3. Assessing the predictive validity of psychomotor tests as measures of biological age in mice.

    PubMed

    Ingram, D K; Reynolds, M A

    1986-01-01

    Two experiments assessed the predictive validity of a psychomotor test battery in male C57BL/6J mice. First, performance was recorded for 66 mice in rotorod, tightrope, grip strength, exploratory activity, and runwheel activity tasks at 24 mo of age. Except in the rotorod task, performance was positively and significantly correlated to lifespan, i.e. better performance indicated longer lifespan. Body weight and body temperature were also significantly correlated with lifespan, while water consumption was negatively related. Using the five behavioral scores in a multiple regression analysis, about 40% of the variance in lifespan was explainable. When measures of body weight, body temperature, and water consumption were added to the regression equation, about 54% of the variance in lifespan could be explained. As revealed by factor analysis, a high degree of interrelationship existed among variables. In a second experiment, 54 mice were tested in the psychomotor battery every 8 weeks from 24 mo. Scores in the tightrope and both locomotor activity tasks revealed age-related declines, whether considering all individuals or only those surviving to 28 mo. Significant correlations between first and subsequent scores indicated stability of individual differences for tightrope and exploratory activity at most ages and for runwheel activity at 26 mo but not later. Rotorod and grip strength scores were not stable and suggested confounding by learning. Significant correlations with lifespan were obtained at some ages for all tests. In contrast to the first experiment, however, there were no significant correlations between lifespan and scores at 24-mo for any test and little correlation among scores.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. Determining Biology Student Teachers' Cognitive Structure on the Concept of "Diffusion" through the Free Word-Association Test and the Drawing-Writing Technique

    ERIC Educational Resources Information Center

    Kurt, Hakan; Ekici, Gülay; Aktas, Murat; Aksu, Özlem

    2013-01-01

    The aim of the current study is to investigate student biology teachers' cognitive structures related to "diffusion" through the free word-association test and the drawing-writing technique. As the research design of the study, the qualitative research method was applied. The data were collected from 44 student biology teachers. The free…

  5. Commercialization of genetic testing services: the FDA, market forces, and biological tarot cards.

    PubMed

    Malinowski, M J; Blatt, R J R

    1997-03-01

    Many women fear being diagnosed with breast cancer, and rightfully so. Despite the capabilities of modern medicine, the cumulative lifetime risk of getting the disease has risen to one in eight and, despite decades of research, no cures exist. In this Article, the authors explore the commercialization of so-called breast cancer gene tests, based upon genetic alterations linked to the disease. Although the authors fully address this specific technology, they use what constitutes the seminal case of predictive genetic testing to analyze the adequacy of the existing regulatory framework. The authors conclude that the present regulatory system is inadequate and places a dangerous amount of reliance on primary care physicians. Their conclusion is grounded in the observation that most primary care physicians lack sufficient knowledge about this evolving investigative technology--which is highly subject to misinterpretation, and, though potentially helpful to some "high risk" patients, offers questionable clinical value for the general public. The authors set forth numerous proposals to promote both the quality and clinical value of predictive genetic testing so that it conforms to public health standards and can be properly integrated as a reliable component of medical care in specific situations.

  6. System development and early biological tests in NASA's biomass production chamber

    NASA Technical Reports Server (NTRS)

    Wheeler, R. M.; Mackowiak, C. L.; Dreschel, T. W.; Sager, J. C.; Prince, R. P.; Knott, W. M.; Hinkle, C. R.; Strayer, R. F.

    1990-01-01

    The Biomass Production Chamber at Kennedy Space Center was constructed to conduct large scale plant growth studies for NASA's CELSS program. Over the past four years, physical systems and computer control software have been continually upgraded and the degree of atmospheric leakage from the chamber has decreased from about 40 to 5 percent of the total volume per day. Early tests conducted with a limited degree of closure showed that total crop (wheat) growth from the best trays was within 80 percent of reported optimal yields for similar light levels. Yields from subsequent tests under more tightly closed conditions have not been as good--up to only 65 percent of optimal yields. Yields appear to have decreased with increasing closure, yet potential problems exist in cultural techniques and further studies are warranted. With the ability to tightly seal the chamber, quantitative data were gathered on CO2 and water exchange rates. Results showed that stand photosynthesis and transpiration reached a peak near 25 days after planting, soon after full vegetative ground cover was established. In the final phase of testing when atmospheric closure was the highest, ethylene gas levels in the chamber rose from about 10 to nearly 120 ppb. Evidence suggests that the ethylene originated from the wheat plants themselves and may have caused an epinastic rolling of the leaves, but no apparent detrimental effects on whole plant function.

  7. Successful lichen translocation on disturbed gypsum areas: A test with adhesives to promote the recovery of biological soil crusts

    PubMed Central

    Ballesteros, M.; Ayerbe, J.; Casares, M.; Cañadas, E. M.; Lorite, J.

    2017-01-01

    The loss of biological soil crusts represents a challenge for the restoration of disturbed environments, specifically in particular substrates hosting unique lichen communities. However, the recovery of lichen species affected by mining is rarely addressed in restoration projects. Here, we evaluate the translocation of Diploschistes diacapsis, a representative species of gypsum lichen communities affected by quarrying. We tested how a selection of adhesives could improve thallus attachment to the substrate and affect lichen vitality (as CO2 exchange and fluorescence) in rainfall-simulation and field experiments. Treatments included: white glue, water, hydroseeding stabiliser, gum arabic, synthetic resin, and a control with no adhesive. Attachment differed only in the field, where white glue and water performed best. Adhesives altered CO2 exchange and fluorescence yield. Notably, wet spoils allowed thalli to bind to the substrate after drying, revealing as the most suitable option for translocation. The satisfactory results applying water on gypsum spoils are encouraging to test this methodology with other lichen species. Implementing these measures in restoration projects would be relatively easy and cost-effective. It would help not only to recover lichen species in the disturbed areas but also to take advantage of an extremely valuable biological material that otherwise would be lost. PMID:28367957

  8. Biologic surveys for the Sandia National Laboratories, Coyote Canyon Test Complex, Kirtland Air Force Base, Albuquerque, New Mexico

    SciTech Connect

    Sullivan, R.M.; Knight, P.J.

    1994-05-25

    This report provides results of a comprehensive biologic survey performed in Coyote Canyon Test Complex (CCTC), Sandia National Laboratories (SNL), Bernalillo County, New Mexico, which was conducted during the spring and summer of 1992 and 1993. CCTC is sited on land owned by the Department of Energy (DOE) and Kirtland Air Force Base and managed by SNL. The survey covered 3,760 acres of land, most of which is rarely disturbed by CCTC operations. Absence of grazing by livestock and possibly native ungulates, and relative to the general condition of private range lands throughout New Mexico, and relative to other grazing lands in central New Mexico. Widely dispersed, low intensity use by SNL as well as prohibition of grazing has probably contributed to abundance of special status species such as grama grass cactus within the CCTC area. This report evaluates threatened and endangered species found in the area, as well as comprehensive assessment of biologic habitats. Included are analyses of potential impacts and mitigative measures designed to reduce or eliminate potential impacts. Included is a summary of CCTC program and testing activities.

  9. [Value of the sleep EEG as a biological marker of depressive states. Comparison with 3 neuroendocrine tests].

    PubMed

    Ansseau, M; Scheyvaerts, M; Doumont, A; Poirrier, R; Demonceau, G; Legros, J J; Franck, G

    1985-04-01

    In a sample of 12 endogenous depressive inpatients (8 primary and 4 secondary depressives), we compared the diagnostic usefulness of REM latency (recorded during at least 4 consecutive nights) with 3 neuroendocrine tests: dexamethasone suppression test and GH response after clonidine (a alpha-adrenergic agonist) and apomorphine (a dopaminergic agonist) challenges. Shortened REM latency (less than 50 min during at least 1 night) was present in 67% of depressives. However, REM latency presented a clear night to night intra-patient variability that makes it necessary to record at least 3 consecutive nights for the best sensitivity. Non-suppression after dexamethasone was present in 50% of depressives, blunted GH response after clonidine, in 75% and blunted response after apomorphine, in 42%. A total of 92% of patients exhibited at least one abnormal biological parameter (100% of primary and 75% of secondary depressives); 67% of patients exhibited at least two disturbed parameters and these patients constituted the whole primary depressive group (100%). These results show that these 4 potential biological markers of depression are not necessarily distributed in the same population. This suggests the potential usefulness of their concurrent use for improved accuracy of diagnosis.

  10. Successful lichen translocation on disturbed gypsum areas: A test with adhesives to promote the recovery of biological soil crusts.

    PubMed

    Ballesteros, M; Ayerbe, J; Casares, M; Cañadas, E M; Lorite, J

    2017-04-03

    The loss of biological soil crusts represents a challenge for the restoration of disturbed environments, specifically in particular substrates hosting unique lichen communities. However, the recovery of lichen species affected by mining is rarely addressed in restoration projects. Here, we evaluate the translocation of Diploschistes diacapsis, a representative species of gypsum lichen communities affected by quarrying. We tested how a selection of adhesives could improve thallus attachment to the substrate and affect lichen vitality (as CO2 exchange and fluorescence) in rainfall-simulation and field experiments. Treatments included: white glue, water, hydroseeding stabiliser, gum arabic, synthetic resin, and a control with no adhesive. Attachment differed only in the field, where white glue and water performed best. Adhesives altered CO2 exchange and fluorescence yield. Notably, wet spoils allowed thalli to bind to the substrate after drying, revealing as the most suitable option for translocation. The satisfactory results applying water on gypsum spoils are encouraging to test this methodology with other lichen species. Implementing these measures in restoration projects would be relatively easy and cost-effective. It would help not only to recover lichen species in the disturbed areas but also to take advantage of an extremely valuable biological material that otherwise would be lost.

  11. Successful lichen translocation on disturbed gypsum areas: A test with adhesives to promote the recovery of biological soil crusts

    NASA Astrophysics Data System (ADS)

    Ballesteros, M.; Ayerbe, J.; Casares, M.; Cañadas, E. M.; Lorite, J.

    2017-04-01

    The loss of biological soil crusts represents a challenge for the restoration of disturbed environments, specifically in particular substrates hosting unique lichen communities. However, the recovery of lichen species affected by mining is rarely addressed in restoration projects. Here, we evaluate the translocation of Diploschistes diacapsis, a representative species of gypsum lichen communities affected by quarrying. We tested how a selection of adhesives could improve thallus attachment to the substrate and affect lichen vitality (as CO2 exchange and fluorescence) in rainfall-simulation and field experiments. Treatments included: white glue, water, hydroseeding stabiliser, gum arabic, synthetic resin, and a control with no adhesive. Attachment differed only in the field, where white glue and water performed best. Adhesives altered CO2 exchange and fluorescence yield. Notably, wet spoils allowed thalli to bind to the substrate after drying, revealing as the most suitable option for translocation. The satisfactory results applying water on gypsum spoils are encouraging to test this methodology with other lichen species. Implementing these measures in restoration projects would be relatively easy and cost-effective. It would help not only to recover lichen species in the disturbed areas but also to take advantage of an extremely valuable biological material that otherwise would be lost.

  12. Field testing of biological spectral weighting functions for induction of UV-absorbing compounds in higher plants.

    PubMed

    Flint, Stephan D; Searles, Peter S; Caldwell, Martyn M

    2004-05-01

    Action spectra are typically used as biological spectral weighting functions (BSWF) in biological research on the stratospheric ozone depletion issue. Despite their critical role in determining the amount of UV supplied in experiments, there has been only limited testing of different functions under realistic field conditions. Here, we calculate effective radiation according to five published BSWF and evaluate the appropriateness of these BSWF in representing the induction of UV-absorbing compounds. Experiments were carried out in the field using both ultraviolet-B radiation (280-320 nm) supplementation and selective filtering of solar UV radiation. For the four species tested, BSWF that extend into the ultraviolet-A radiation (320-400 nm) (UV-A) with moderate effectiveness best represented the observed results. When compared with the commonly used generalized plant response, these BSWF suggest that simulations of ozone depletion will require more radiation than in the past experiments. However, they imply lower radiation supplements than a new plant growth BSWF that has a greater emphasis on UV-A wavelengths.

  13. Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

    PubMed Central

    Bouskill, Nicholas J.; Tang, Jinyun; Riley, William J.; Brodie, Eoin L.

    2012-01-01

    Trait-based microbial models show clear promise as tools to represent the diversity and activity of microorganisms across ecosystem gradients. These models parameterize specific traits that determine the relative fitness of an “organism” in a given environment, and represent the complexity of biological systems across temporal and spatial scales. In this study we introduce a microbial community trait-based modeling framework (MicroTrait) focused on nitrification (MicroTrait-N) that represents the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) using traits related to enzyme kinetics and physiological properties. We used this model to predict nitrifier diversity, ammonia (NH3) oxidation rates, and nitrous oxide (N2O) production across pH, temperature, and substrate gradients. Predicted nitrifier diversity was predominantly determined by temperature and substrate availability, the latter was strongly influenced by pH. The model predicted that transient N2O production rates are maximized by a decoupling of the AOB and NOB communities, resulting in an accumulation and detoxification of nitrite to N2O by AOB. However, cumulative N2O production (over 6 month simulations) is maximized in a system where the relationship between AOB and NOB is maintained. When the reactions uncouple, the AOB become unstable and biomass declines rapidly, resulting in decreased NH3 oxidation and N2O production. We evaluated this model against site level chemical datasets from the interior of Alaska and accurately simulated NH3 oxidation rates and the relative ratio of AOA:AOB biomass. The predicted community structure and activity indicate (a) parameterization of a small number of traits may be sufficient to broadly characterize nitrifying community structure and (b) changing decadal trends in climate and edaphic conditions could impact nitrification rates in ways that are not captured by extant biogeochemical models. PMID

  14. Testing the effectiveness of problem-based learning with learning-disabled students in biology

    NASA Astrophysics Data System (ADS)

    Guerrera, Claudia Patrizia

    The purpose of the present study was to investigate the effects of problem-based learning (PBL) with learning-disabled (LD) students. Twenty-four students (12 dyads) classified as LD and attending a school for the learning-disabled participated in the study. Students engaged in either a computer-based environment involving BioWorld, a hospital simulation designed to teach biology students problem-solving skills, or a paper-and-pencil version based on the computer program. A hybrid model of learning was adopted whereby students were provided with direct instruction on the digestive system prior to participating in a problem-solving activity. Students worked in dyads and solved three problems involving the digestive system in either a computerized or a paper-and-pencil condition. The experimenter acted as a coach to assist students throughout the problem-solving process. A follow-up study was conducted, one month later, to measure the long-term learning gains. Quantitative and qualitative methods were used to analyze three types of data: process data, outcome data, and follow-up data. Results from the process data showed that all students engaged in effective collaboration and became more systematic in their problem solving over time. Findings from the outcome and follow-up data showed that students in both treatment conditions, made both learning and motivational gains and that these benefits were still evident one month later. Overall, results demonstrated that the computer facilitated students' problem solving and scientific reasoning skills. Some differences were noted in students' collaboration and the amount of assistance required from the coach in both conditions. Thus, PBL is an effective learning approach with LD students in science, regardless of the type of learning environment. These results have implications for teaching science to LD students, as well as for future designs of educational software for this population.

  15. Host range testing and biology of Abia sericea (Cimbicidae), a candidate for biological control of invasive teasels (Dipsacus spp.) in North America

    USDA-ARS?s Scientific Manuscript database

    Invasive teasels (Dipsacus spp., Dipsacaceae) are widespread in the USA, being present in 43 states and listed as noxious in five. The cimbicid sawfly Abia sericea (L.) is under evaluation as a potential agent for biological control of teasels. The host range, biology, and life history of this ins...

  16. Thresholded Two-Phase Test Sample Representation for Outlier Rejection in Biological Recognition

    PubMed Central

    Wu, Xiang; Wu, Ning

    2013-01-01

    The two-phase test sample representation (TPTSR) was proposed as a useful classifier for face recognition. However, the TPTSR method is not able to reject the impostor, so it should be modified for real-world applications. This paper introduces a thresholded TPTSR (T-TPTSR) method for complex object recognition with outliers, and two criteria for assessing the performance of outlier rejection and member classification are defined. The performance of the T-TPTSR method is compared with the modified global representation, PCA and LDA methods, respectively. The results show that the T-TPTSR method achieves the best performance among them according to the two criteria. PMID:23554837

  17. Study of the genotoxicity of organic extracts from wastewater-irrigated vegetables using in vitro and in vivo biological tests.

    PubMed

    Gao, Hongxia; Cao, Yanhua; Liu, Yingli; Liu, Nan; Guan, Weijun

    2017-03-01

    The purpose of this study was to explore genotoxicity due to organic pollutants in wastewater-irrigated vegetables using biological and chemical analyses. Chinese cabbages from wastewater-irrigated farmland were taken as the research object. For the in vitro test, DNA damage was characterized in rat hepatocytes exposed to organic extracts from the cabbages using the comet assay. For the in vivo tests, mice were exposed to organic extracts from the cabbages. DNA damage was assessed in mouse peripheral blood lymphocytes (PBLs), and chromosome damage was assessed in bone marrow cells using the comet assay and micronucleus test, respectively. For the chemical analysis, gas chromatography-mass spectrometry (GC/MS) was used to analyze the organic compounds in the organic vegetable extracts. The in vitro test results showed that the comet tail lengths of the DNA in rat hepatocytes were significantly increased in the group dosed with 0.36 g/ml (P < 0.05), and the comet tailing rates of the hepatocytes were significantly increased in the groups dosed with 0.24 and 0.36 g/ml (P < 0.05). The in vivo test results indicated that the comet tail lengths of the DNA in mouse PBLs were increased in the low- and high-dose groups and that the comet tailing rate of the PBLs was increased in the high-dose group (P < 0.05). The chemical analysis results showed that the total organic content in the organic vegetable extracts from the wastewater-irrigated area (1.355 mg/kg) was significantly higher than the content in the cabbage samples from the clean-water-irrigated area (0.089 mg/kg). This finding indicated that wastewater irrigation can cause organic pollution with genetic toxicity in vegetables. This study also showed that in vivo and in vitro biological tests can reflect the joint toxicity of organic pollutants, and the test results were in accordance with the chemical analysis of the organic pollutant compositions.

  18. Photodegradation of fluorene in aqueous solution: Identification and biological activity testing of degradation products.

    PubMed

    Kinani, Said; Souissi, Yasmine; Kinani, Aziz; Vujović, Svetlana; Aït-Aïssa, Sélim; Bouchonnet, Stéphane

    2016-04-15

    Degradation of fluorene under UV-vis irradiation in water was investigated and structural elucidation of the main photoproducts was achieved using gas chromatography coupled with mass spectrometry. Twenty-six photoproducts were structurally identified, mainly on the basis of electron ionization mass spectra interpretation. The main generated transformation products are hydroxy derivatives. Some secondary photoproducts including fluorenone, hydroxy fluorenone, 2-biphenyl carboxylic acid, biphenylene, methanol fluorene congeners and hydroxy fluorene dimers were also observed. A photodegradation pathway was suggested on the basis of the chemical structures of photoproducts. Fluorene as well as its main photoproducts for which chemical standards were commercially available were tested for their ability to elicit cytotoxic, estrogenic and dioxin-like activity by using in vitro cell-based bioassays. None of the tested compounds was cytotoxic at concentrations up to 100 μM. However, 2-hydroxyfluorene and 3-hydroxyfluorene exerted significant estrogenic and dioxin-like activity on a concentration range of 3-30 μM, while fluorene and 9-hydroxyfluorene were weakly or not active, respectively, in our assays. This supports the view that photodegradation processes can generate by-products of higher toxicological concern than the parent compound and strengthens the need to further identify transformation products in the aquatic environment. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Biological induced corrosion of materials II: New test methods and experiences from mir station

    NASA Astrophysics Data System (ADS)

    Klintworth, R.; Reher, H. J.; Viktorov, A. N.; Bohle, D.

    1999-09-01

    During previous long-term manned missions, more than 100 species of microorganisms have been identified on surfaces of materials (bacteria and fungi). Among them were potentially pathogenic ones (saprophytes) which are capable of active growth on artificial substrates, as well as technophilic bacteria and fungi causing damages (destruction and degradation) to various materials (metals and polymers), resulting in failures and disruptions in the functioning of equipment and hardware. Aboard a space vehicle some microclimatic parameters are optimal for microorganism growth: the atmospheric fluid condensate with its specific composition, chemical and/or antropogenic contaminants (human metobolic products, etc.) all are stimulating factors for the development of bacteria and mould fungi on materials of the interior and equipment of an orbital station during its operational phase(s). Especially Russian long-term missions (SALJUT, MIR) have demonstrated that uncontrolled interactions of microorganisms with materials will ultimately lead to the appearence of technological and medical risks, significantly influencing safety and reliability characteristics of individual as well as whole systems and/ or subsystems. For a first conclusion, it could be summarized, that countermeasures and anti-strategies focussing on Microbial Contamination Management (MCM) for the International Space Station (ISS, next long-term manned mission) at least require a new materials test approach. Our respective concept includes a combined age-ing/biocorrosion test sequence. It is represented here, as well as current status of MCM program, e.g. continuous monitoring (microbiological analyses), long-term disinfection, frequent cleaning methods, mathematical modeling of ISS, etc.

  20. Relationships among sediment chemistry, toxicity testing, and biology: What can large-scale monitoring teach us?

    SciTech Connect

    Summers, J.K.; Macauley, J.M.; Engle, V.D.; Malaeb, Z.

    1995-12-31

    The Environmental Monitoring and Assessment Program for Estuarine Resources has collected sediments from over 1,000 varying locations in the estuaries of the United States. At each of these sites, sediments are analyzed for bulk chemistry, tested for toxicity to Ampelisca abdita, and enumerated regarding benthic community structure and abundance. In addition, tissue residues have been examined for selected fish and shellfish species and toxicity testing has been completed at selected sites for alternative species. The statistical and ecological relationships among these indicators have been examined with regard to how they can used to identify the overall ecological condition of a site, an estuary, or populations of estuaries. Comparisons of these relationships among different regions of the country show major differences in the modes of exposure and response being prevalent in the Southeast and Gulf Coasts as compared to the Mid-Atlantic and West Coasts. While the extent of sediment contamination in the Southeast and Gulf estuaries appears to be similar to that of the Mid-Atlantic and California Coasts, the degree of contamination at contaminated sites is much greater in Mid-Atlantic estuaries. An examination of the primary contaminants suggests that the primary sources of contamination in the Mid-Atlantic are industrial and urban while the Southeast and Gulf estuaries are dominated by agricultural contaminants.