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  • Articles  (230)
  • Molecular Diversity Preservation International  (181)
  • American Institute of Physics (AIP)
  • Cambridge University Press
  • 2015-2019  (230)
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  • Articles  (230)
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  • 11
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    Exits in order: How crowding affects particle lifetimes (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-06-28
    Description: Diffusive processes are often represented using stochastic random walk frameworks. The amount of time taken for an individual in a random walk to intersect with an absorbing boundary is a fundamental property that is often referred to as the particle lifetime, or the first passage time. The mean lifetime of particles in a random walk model of diffusion is related to the amount of time required for the diffusive process to reach a steady state. Mathematical analysis describing the mean lifetime of particles in a standard model of diffusion without crowding is well known. However, the lifetime of agents in a random walk with crowding has received much less attention. Since many applications of diffusion in biology and biophysics include crowding effects, here we study a discrete model of diffusion that incorporates crowding. Using simulations, we show that crowding has a dramatic effect on agent lifetimes, and we derive an approximate expression for the mean agent lifetime that includes crowding effects. Our expression matches simulation results very well, and highlights the importance of crowding effects that are sometimes overlooked.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 12
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    Concentric nano rings observed on Al-Cu-Fe microspheres (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-06-03
    Description: It is well known that when particle size is reduced, surface effect becomes important. As a result, micro/nanoparticles tend to have well defined geometric shapes to reduce total surface energy, as opposed to the irregular shapes observed in most bulk materials. The surface of such micro/nanostructures are smooth. Any deviation from a smooth surface implies an increased surface energy which is not energetically favorable. Here, we report an observation of spherical particles in an alloy of Al 65 Cu 20 Fe 15 nominal composition prepared by arc melting. Such spherical particles stand out from those reported so far due to the decoration of concentric nanorings on the surface. Three models for the formation of these concentric ring patterns are suggested. The most prominent ones assume that the rings are frozen features of liquid motion which could open the door to investigate the kinetics of liquid motion on the micro/nanometer scale.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 13
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    Electron plasma dynamics during autoresonant excitation of the diocotron mode (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-02-04
    Description: Chirped-frequency autoresonant excitation of the diocotron mode is used to move electron plasmas confined in a Penning-Malmberg trap across the magnetic field for advanced plasma and antimatter applications. Plasmas of 10 8 electrons, with radii small compared to that of the confining electrodes, can be moved from the magnetic axis to ≥90% of the electrode radius with near unit efficiency and reliable angular positioning. Translations of ≥70% of the wall radius are possible for a wider range of plasma parameters. Details of this process, including phase and displacement oscillations in the plasma response and plasma expansion, are discussed, as well as possible extensions of the technique.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 14
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    An adaptive multi-level simulation algorithm for stochastic biological systems (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-01-14
    Description: Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10 (1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ . This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 15
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    Nonlinear forecasting of intertidal shoreface evolution (2015)
    American Institute of Physics (AIP)
    In: Chaos
    Details
    Publication Date: 2015-10-01
    Description: Natural systems dominated by sediment transport are notoriously difficult to forecast. This is particularly true along the ocean coastline, a region that draws considerable human attention as economic investment and infrastructure are threatened by both persistent, long-term and acute, event driven processes (i.e., sea level rise and storm damage, respectively). Forecasting the coastline's evolution over intermediate time (daily) and space (tens of meters) scales is hindered by the complexity of sediment transport and hydrodynamics, and limited access to the detailed local forcing that drives fast scale processes. Modern remote sensing systems provide an efficient, economical means to collect data within these regions. A solar-powered digital camera installation is used to capture the coast's evolution, and machine learning algorithms are implemented to extract the shoreline and estimate the daily mean intertidal coastal profile. Methods in nonlinear time series forecasting and genetic programming applied to these data corroborate that coastal morphology at these scales is predominately driven by nonlinear internal dynamics, which partially mask external forcing signatures. Results indicate that these forecasting techniques achieve nontrivial predictive skill for spatiotemporal forecast of the upper coastline profile (as much as 43% of variance in data explained for one day predictions). This analysis provides evidence that societally relevant coastline forecasts can be achieved without knowing the forcing environment or the underlying dynamical equations that govern coastline evolution.
    Print ISSN: 1054-1500
    Electronic ISSN: 1089-7682
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 16
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    Tailoring diffuse reflectance of inhomogeneous films containing microplatelets (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-10-07
    Description: We develop an analytical model for calculating the diffuse reflectance of inhomogeneous films containing aligned microplatelets with diameters much greater than the wavelength. The scattering parameters are derived by modeling the platelets as one-dimensional thin films, and the overall diffuse reflectance of the slab is calculated using the Kubelka-Munk model. Our model predicts that reflection minima and maxima arising from coherent interference within the platelets are preserved in the diffuse reflectance of the disordered slab. Experimental validation of the model is provided by reflectance measurements (0.3–15  μ m) of a solid aerosol film of aligned hexagonal boron nitride platelets.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 17
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    Impacts of gastropods on epiphytic microalgae on the brown macroalga Himantothallus grandifolius (2019)
    Cambridge University Press
    Details
    Publication Date: 2019
    Description: 〈div data-abstract-type="normal"〉〈p〉Chemically defended benthic macroalgae that dominate shallow, hard bottom communities along the western Antarctic Peninsula support very high densities of mesograzers, particularly amphipods but also small gastropods. Previous studies have demonstrated that the macroalgae and amphipods form a mutualistic relationship. The chemically defended macroalgae provide the amphipods with a refuge from predation while the macroalgae benefit from the amphipods greatly reducing surface fouling by smaller algae. One of the three most important macroalgae in terms of overstory cover, 〈span〉Himantothallus grandifolius〈/span〉, forms huge blades that can carpet the benthos. Field observations suggest that gastropods may be higher in relative abundance in proportion to amphipods on 〈span〉H. grandifolius〈/span〉 than on other overstory macroalgae. The present study documents the finding that natural abundances of gastropods on 〈span〉H. grandifolius〈/span〉 maintained in mesocosms reduce fouling by microscopic algae, primarily diatoms. However, amphipods are probably also important in keeping the macroalga clean of diatoms in nature. In a smaller scale experiment, three gastropod species were differentially effective at reducing diatom coverage on 〈span〉H. grandifolius.〈/span〉 The hypothesis that gastropods benefit from associating with 〈span〉H. grandifolius〈/span〉 in potentially gaining a refuge from sea-star predation was also tested but not supported by the experimental results.〈/p〉〈/div〉
    Print ISSN: 0954-1020
    Electronic ISSN: 1365-2079
    Topics: Biology , Geography , Geosciences
    Published by Cambridge University Press on behalf of Antarctic Science Ltd.
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  • 18
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    Reanalysis of the US Geological Survey Benchmark Glaciers: long-term insight into climate forcing of glacier mass balance (2019)
    Cambridge University Press
    Details
    Publication Date: 2019
    Description: 〈div data-abstract-type="normal"〉〈p〉Mountain glaciers integrate climate processes to provide an unmatched signal of regional climate forcing. However, extracting the climate signal via intercomparison of regional glacier mass-balance records can be problematic when methods for extrapolating and calibrating direct glaciological measurements are mixed or inconsistent. To address this problem, we reanalyzed and compared long-term mass-balance records from the US Geological Survey Benchmark Glaciers. These five glaciers span maritime and continental climate regimes of the western United States and Alaska. Each glacier exhibits cumulative mass loss since the mid-20th century, with average rates ranging from −0.58 to −0.30 m w.e. a〈span〉−1〈/span〉. We produced a set of solutions using different extrapolation and calibration methods to inform uncertainty estimates, which range from 0.22 to 0.44 m w.e. a〈span〉−1〈/span〉. Mass losses are primarily driven by increasing summer warming. Continentality exerts a stronger control on mass loss than latitude. Similar to elevation, topographic shading, snow redistribution and glacier surface features often exert important mass-balance controls. The reanalysis underscores the value of geodetic calibration to resolve mass-balance magnitude, as well as the irreplaceable value of direct measurements in contributing to the process-based understanding of glacier mass balance.〈/p〉〈/div〉
    Print ISSN: 0022-1430
    Electronic ISSN: 1727-5652
    Topics: Geography , Geosciences
    Published by Cambridge University Press on behalf of The International Glaciological Society (IGS).
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  • 19
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    An adaptive multi-level simulation algorithm for stochastic biological systems (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-01-14
    Description: Discrete-state, continuous-time Markov models are widely used in the modeling of biochemical reaction networks. Their complexity often precludes analytic solution, and we rely on stochastic simulation algorithms (SSA) to estimate system statistics. The Gillespie algorithm is exact, but computationally costly as it simulates every single reaction. As such, approximate stochastic simulation algorithms such as the tau-leap algorithm are often used. Potentially computationally more efficient, the system statistics generated suffer from significant bias unless tau is relatively small, in which case the computational time can be comparable to that of the Gillespie algorithm. The multi-level method [Anderson and Higham, “Multi-level Monte Carlo for continuous time Markov chains, with applications in biochemical kinetics,” SIAM Multiscale Model. Simul. 10 (1), 146–179 (2012)] tackles this problem. A base estimator is computed using many (cheap) sample paths at low accuracy. The bias inherent in this estimator is then reduced using a number of corrections. Each correction term is estimated using a collection of paired sample paths where one path of each pair is generated at a higher accuracy compared to the other (and so more expensive). By sharing random variables between these paired paths, the variance of each correction estimator can be reduced. This renders the multi-level method very efficient as only a relatively small number of paired paths are required to calculate each correction term. In the original multi-level method, each sample path is simulated using the tau-leap algorithm with a fixed value of τ . This approach can result in poor performance when the reaction activity of a system changes substantially over the timescale of interest. By introducing a novel adaptive time-stepping approach where τ is chosen according to the stochastic behaviour of each sample path, we extend the applicability of the multi-level method to such cases. We demonstrate the efficiency of our method using a number of examples.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 20
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    Lake-level variability in Salar de Coipasa, Bolivia during the past ∼40,000 yr (2018)
    Cambridge University Press
    Details
    Publication Date: 2018
    Description: 〈div data-abstract-type="normal"〉〈p〉Various paleoclimatic records have been used to reconstruct the hydrologic history of the Altiplano, relating this history to past variability of the South American summer monsoon. Prior studies of the southern Altiplano, the location of the world’s largest salt flat, the Salar de Uyuni, and its neighbor, the Salar de Coipasa, generally agree in their reconstructions of the climate history of the past ∼24 ka. Some studies, however, have highly divergent climatic records and interpretations of earlier periods. In this study, lake-level variation was reconstructed from a ∼14-m-long sediment core from the Salar de Coipasa. These sediments span the last ∼40 ka. Lacustrine sediment accumulation was apparently continuous in the basin from ∼40 to 6 ka, with dry or very shallow conditions afterward. The fossil diatom stratigraphy and geochemical data (δ〈span〉13〈/span〉C, δ〈span〉15〈/span〉N, %Ca, C/N) indicate fluctuations in lake level from shallow to moderately deep, with the deepest conditions correlative with the Heinrich-1 and Younger Dryas events. The stratigraphy shows a continuous lake of variable depth and salinity during the last glacial maximum and latter stages of Marine Oxygen Isotope Stage 3 and is consistent with environmental inferences and the original chronology of a drill core from Salar de Uyuni.〈/p〉〈/div〉
    Print ISSN: 0033-5894
    Electronic ISSN: 1096-0287
    Topics: Geography , Geosciences
    Published by Cambridge University Press
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