Microscale Processes Research Articles

Structural and petrophysical effects of overthrusting on highly porous sandstones: the Aztec Sandstone in the Buffington window, SE Nevada, USA

Abstract Little is known about the effect of thrusting on lithological and petrophysical properties of reservoir sandstone. Here we use field observations, probe permeability measurements and thin-section analysis along ten transects from the Muddy Mountain thrust contact downwards into the underlying Jurassic Aztec Sandstone to evaluate the nature and extent of petrophysical and microstructural changes caused by the thrusting. The results reveal a decimetre- to metre-thick low-permeable (≤50 mD) and indurated (0–3% porosity) zone immediately beneath the thrust contact in which dominant microscale processes, in decreasing order of importance, are (1) cataclasis with local fault gouge formation; (2) pressure solution; and (3) very limited cementation. From this narrow zone the petrophysical and microstructural effect of the thrusting decreases gradually downwards into a friable, highly porous ( c. 25%) and permeable (≤2 D) sandstone some 50–150 m below the thrust, in which strain is localized into deformation band populations. In general, the petrophysical properties of the sandstone as a result of overthrusting reveal little impact in overall primary reservoir quality below some tens of metres into the footwall, except for the relatively minor baffling effect of deformation bands.

Particle packing and rheology of cement pastes at different replacement levels of cement by α-Al2O3 submicron particles

The aim of this study was to clarify the micro-scale processes which control the fresh and hardened properties of hydrating cement pastes containing up to 10wt% of α-Al2O3 submicron particles and a polycarboxylate-type superplasticizer. The main factor controlling the changes in the microstructure and properties of the fresh pastes with increasing α-Al2O3 cement replacement levels was found to be the increase in the total specific surface area, whereas particle packing played only a minor role. However, in the case of the hardened pastes much more complex and somewhat counteracting effects were observed. Depending on the cement replacement level of the pastes, the sum of these effects was either a hardly noticeable improvement in their mechanical properties, compared to those of the reference paste, or even a reduction in them. These differences decreased with increasing curing time.

Evaluating the local socio-economic impact of redevelopments using shift-share analysis: a case study of destination redevelopments in Las Vegas (1990–2010)

Monitoring neighbourhood change associated with a redevelopment is important for policy-makers, business leaders and residents. It helps evaluate public policy and changes in the needs of residents and businesses. However, using raw data (e.g. census data) to track such changes can be problematic. It does not allow one to distinguish between trends attributable to macro- and micro-scale processes. This paper demonstrates how a novel neighbourhood-level, GIS-based spatial approach using shift-share analysis can help resolve this issue. To illustrate its utility, this technique is used to examine the local socio-economic impact of destination redevelopments in Las Vegas between 1990 and 2010.

Numerical Simulation of Thrombotic Occlusion in Tortuous Arterioles

Tortuous microvessels alter blood flow and stimulate thrombosis but the physical mechanisms are poorly understood. Both tortuous microvessels and abnormally large platelets are seen in diabetic patients. Thus, the objective of this study was to determine the physical effects of arteriole tortuosity and platelet size on the microscale processes of thrombotic occlusion in microvessels. A new lattice-Boltzmann method-based discrete element model was developed to simulate the fluid flow field with fluid-platelet coupling, platelet interactions, thrombus formation, and thrombotic occlusion in tortuous arterioles. Our results show that vessel tortuosity creates high shear stress zones that activate platelets and stimulate thrombus formation. The growth rate depends on the level of tortuosity and the pressure and flow boundary conditions. Once thrombi began to form, platelet collisions with thrombi and subsequent activations were more important than tortuosity level. Thrombus growth narrowed the channel and reduced the flow rate. Larger platelet size leads to quicker decrease of flow rate due to larger thrombi that occluded the arteriole. This study elucidated the important roles that tortuosity and platelet size play in thrombus formation and occlusion in arterioles.

Simulations and analysis of multiphase transport and reaction in segmented flow microreactors

We present volume-of-fluid (VOF) based simulations of coupled transport and reaction processes in microscale segmented flow microreactors. The simulations implemented in OpenFOAM accurately capture the circulation patterns and micron-scale wetting film of the segmented flow. The accurate prediction of the interfacial concentration discontinuity is shown to depend on the local Peclet number. The integrated computational fluid dynamics (CFD) and mass transfer simulations provide complete spatial and temporal information about the concentration field within the reactor, which enable quantification of the mass transfer coefficient kLa as a function of time and operating condition. Mass transport in the segmented flow system is shown to be a two-regime process, dominated first by convection and then by diffusion. Scaling analysis provide a means for estimating mass transfer coefficients and give insights into how to select optimal operating conditions in segmented flow reactors. Finally, we predict mass transfer in segmented flow with reaction, specifically, the mass transfer enhancement as a function of the Damköhler number.

Resolving colocalization of bacteria and metal(loid)s on plant root surfaces by combining fluorescence in situ hybridization (FISH) with multiple-energy micro-focused X-ray fluorescence (ME μXRF)

Metal(loid)-contamination of the environment due to anthropogenic activities is a global problem. Understanding the fate of contaminants requires elucidation of biotic and abiotic factors that influence metal(loid) speciation from molecular to field scales. Improved methods are needed to assess micro-scale processes, such as those occurring at biogeochemical interfaces between plant tissues, microbial cells, and metal(loid)s. Here we present an advanced method that combines fluorescence in situ hybridization (FISH) with synchrotron-based multiple-energy micro-focused X-ray fluorescence microprobe imaging (ME μXRF) to examine colocalization of bacteria and metal(loid)s on root surfaces of plants used to phytostabilize metalliferous mine tailings. Bacteria were visualized on a small root section using SytoBC nucleic acid stain and FISH probes targeting the domain Bacteria and a specific group (Alphaproteobacteria, Gammaproteobacteria, or Actinobacteria). The same root region was then analyzed for elemental distribution and metal(loid) speciation of As and Fe using ME μXRF. The FISH and ME μXRF images were aligned using ImageJ software to correlate microbiological and geochemical results. Results from quantitative analysis of colocalization show a significantly higher fraction of As colocalized with Fe-oxide plaques on the root surfaces (fraction of overlap 0.49±0.19) than to bacteria (0.072±0.052) (p<0.05). Of the bacteria that colocalized with metal(loid)s, Actinobacteria, known for their metal tolerance, had a higher correlation with both As and Fe than Alphaproteobacteria or Gammaproteobacteria. This method demonstrates how coupling these micro-techniques can expand our understanding of micro-scale interactions between roots, metal(loid)s and microbes, information that should lead to improved mechanistic models of metal(loid) speciation and fate.

Micro and Macroscale Drivers of Nutrient Concentrations in Urban Streams in South, Central and North America.

Global metrics of land cover and land use provide a fundamental basis to examine the spatial variability of human-induced impacts on freshwater ecosystems. However, microscale processes and site specific conditions related to bank vegetation, pollution sources, adjacent land use and water uses can have important influences on ecosystem conditions, in particular in smaller tributary rivers. Compared to larger order rivers, these low-order streams and rivers are more numerous, yet often under-monitored. The present study explored the relationship of nutrient concentrations in 150 streams in 57 hydrological basins in South, Central and North America (Buenos Aires, Curitiba, São Paulo, Rio de Janeiro, Mexico City and Vancouver) with macroscale information available from global datasets and microscale data acquired by trained citizen scientists. Average sub-basin phosphate (P-PO4) concentrations were found to be well correlated with sub-basin attributes on both macro and microscales, while the relationships between sub-basin attributes and nitrate (N-NO3) concentrations were limited. A phosphate threshold for eutrophic conditions (>0.1 mg L-1 P-PO4) was exceeded in basins where microscale point source discharge points (eg. residential, industrial, urban/road) were identified in more than 86% of stream reaches monitored by citizen scientists. The presence of bankside vegetation covaried (rho = –0.53) with lower phosphate concentrations in the ecosystems studied. Macroscale information on nutrient loading allowed for a strong separation between basins with and without eutrophic conditions. Most importantly, the combination of macroscale and microscale information acquired increased our ability to explain sub-basin variability of P-PO4 concentrations. The identification of microscale point sources and bank vegetation conditions by citizen scientists provided important information that local authorities could use to improve their management of lower order river ecosystems.

The outflow of ionospheric nitrogen ions: A possible tracer for the altitude‐dependent transport and energization processes of ionospheric plasma

AbstractThough limited, the existing observational data set indicates that N+ is a significant ion in the ionosphere, and its concentration varies with season, time of day, solar cycle, latitude, and geomagnetic conditions. Knowledge of the differential transport of heavy versus light ionospheric species can provide the connection between the macroscale dynamics and microscale processes that govern the near‐Earth space. The mass distribution of accelerated ionospheric ions reflects the source region of the low‐altitude ion composition, and the minor ion component can serve as a tracer of ionospheric processes since they can have a significant influence on the local plasma dynamics.

Coupled lattice Boltzmann method for numerical simulations of fully coupled heart and torso bidomain system in electrocardiology

In this work, a modified coupling Lattice Boltzmann Model (LBM) in simulation of cardiac electrophysiology is developed in order to capture the detailed activities of macro- to micro-scale transport processes. The propagation of electrical activity in the human heart through torso is mathematically modeled by bidomain type systems. As transmembrane potential evolves, we take into account domain anisotropical properties using intracellular and extracellular conductivity, such as in a pacemaker or an electrocardiogram, in both parallel and perpendicular directions to the fibers. The bidomain system represents multi-scale, stiff and strongly nonlinear coupled reaction-diffusion models that consist of a set of ordinary differential equations coupled with a set of partial differential equations. Due to dynamic and geometry complexity, numerical simulation and implementation of bidomain type systems are extremely challenging conceptual and computational problems but are very important in many real-life and biomedical applications. This paper suggests a modified LBM scheme, reliable, efficient, stable and easy to implement in the context of such bidomain systems. Numerical tests to confirm effectiveness and accuracy of our approach are provided and the propagation of electrophysiological waves in the heart is analyzed.

Tensile stress relaxation in unsaturated granular materials

The mechanics of granular media at low liquid saturation levels remain poorly understood. Macroscopic mechanical properties are affected by microscale forces and processes, such as capillary forces, inter-particle friction, liquid flows, and particle movements. An improved understanding of these microscale mechanisms is important for a range of industrial applications and natural phenomena (e.g. landslides). This study focuses on the transient evolution of the tensile stress of unsaturated granular media under extension. Experimental results suggest that the stress state of the material evolves even after cessation of sample extension. Moreover, we observe that the packing density strongly affects the efficiency of different processes that result in tensile stress relaxation. By comparing the observed relaxation time scales with published data, we conclude that tensile stress relaxation is governed by particle rearrangement and fluid redistribution. An increased packing density inhibits particle rearrangement and only leaves fluid redistribution as the major process that governs tensile stress relaxation.

Thermodynamic analysis of gas flow and heat transfer in microchannels

Thermodynamic analysis, especially the second-law analysis, has been applied in engineering design and optimization of microscale gas flow and heat transfer. However, following the traditional approaches may lead to decreased total entropy generation in some microscale systems. The present work reveals that the second-law analysis of microscale gas flow and heat transfer should include both the classical bulk entropy generation and the interfacial one which was usually missing in the previous studies. An increase of total entropy generation will thus be obtained. Based on the kinetic theory of gases, the mathematical expression is provided for interfacial entropy generation, which shows proportional to the magnitude of boundary velocity slip and temperature jump. Analyses of two classical cases demonstrate validity of the new formalism. For a high-Kn flow and heat transfer, the increase of interfacial transport irreversibility dominates. The present work may promote understanding of thermodynamics in microscale heat and fluid transport, and throw light on thermodynamic optimization of microscale processes and systems.

On the scale dependence of earthquake stress drop

We discuss the debated issue of scale dependence in earthquake source mechanics with the goal of providing supporting evidence to foster the adoption of a coherent interpretative framework. We examine the heterogeneous distribution of source and constitutive parameters during individual ruptures and their scaling with earthquake size. We discuss evidence that slip, slip-weakening distance and breakdown work scale with seismic moment and are interpreted as scale dependent parameters. We integrate our estimates of earthquake stress drop, computed through a pseudo-dynamic approach, with many others available in the literature for both point sources and finite fault models. We obtain a picture of the earthquake stress drop scaling with seismic moment over an exceptional broad range of earthquake sizes (−8 < MW < 9). Our results confirm that stress drop values are scattered over three order of magnitude and emphasize the lack of corroborating evidence that stress drop scales with seismic moment. We discuss these results in terms of scale invariance of stress drop with source dimension to analyse the interpretation of this outcome in terms of self-similarity. Geophysicists are presently unable to provide physical explanations of dynamic self-similarity relying on deterministic descriptions of micro-scale processes. We conclude that the interpretation of the self-similar behaviour of stress drop scaling is strongly model dependent. We emphasize that it relies on a geometric description of source heterogeneity through the statistical properties of initial stress or fault-surface topography, in which only the latter is constrained by observations.

Underwater microscopy for in situ studies of benthic ecosystems.

Microscopic-scale processes significantly influence benthic marine ecosystems such as coral reefs and kelp forests. Due to the ocean's complex and dynamic nature, it is most informative to study these processes in the natural environment yet it is inherently difficult. Here we present a system capable of non-invasively imaging seafloor environments and organisms in situ at nearly micrometre resolution. We overcome the challenges of underwater microscopy through the use of a long working distance microscopic objective, an electrically tunable lens and focused reflectance illumination. The diver-deployed instrument permits studies of both spatial and temporal processes such as the algal colonization and overgrowth of bleaching corals, as well as coral polyp behaviour and interspecific competition. By enabling in situ observations at previously unattainable scales, this instrument can provide important new insights into micro-scale processes in benthic ecosystems that shape observed patterns at much larger scales.

Micro-dynamics and macro-patterns: Exploring new archaeological data for the late Holocene human-water relationship in the Murghab alluvial fan, Turkmenistan

In this article we re-visit hypotheses about the changing social and environmental landscapes in southern Central Asia during the late Holocene, specifically giving attention to the transitional period between the archaeologically-defined Late Bronze – Early Iron Age (second half of the 2nd millennium BC) and the numerous documented changes in the archaeological and physio-geographical record during this time. We focus on the northeastern Murghab alluvial fan (Turkmenistan) as a window into this complex period, and examine one aspect of human-environmental dynamics there, namely, the relationship between the location of archaeological sites and mapped ancient watercourses (palaeochannels) through time. Our analysis incorporates nearly 400 new archaeological sites documented in the northeastern Murghab since 2006, which have not previously been included in published models of settlement and/or hydrological dynamics. Our findings suggest the periods of the Late Bronze Age and Early Iron Age (Yaz I) demonstrate two distinct access-to-water practices, which may correlate to different processes of socio-territorial control being implemented. While no single line of evidence can adequately disentangle the complex interconnected processes of environmental and social change, our results lend themselves to integration with the current working knowledge of the local processes of socio-environmental development in the Murghab. The results also fit more broadly within emerging discourse that recognizes the importance of micro-scale processes and adaptation in Eurasian prehistory.

A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals.

Coral reefs, and the unique ecosystems they support, are facing severe threats by human activities and climate change. Our understanding of these threats is hampered by the lack of robust approaches for studying the micro-scale interactions between corals and their environment. Here we present an experimental platform, coral-on-a-chip, combining micropropagation and microfluidics to allow direct microscopic study of live coral polyps. The small and transparent coral micropropagates are ideally suited for live-imaging microscopy, while the microfluidic platform facilitates long-term visualization under controlled environmental conditions. We demonstrate the usefulness of this approach by imaging coral micropropagates at previously unattainable spatio-temporal resolutions, providing new insights into several micro-scale processes including coral calcification, coral–pathogen interaction and the loss of algal symbionts (coral bleaching). Coral-on-a-chip thus provides a powerful method for studying coral physiology in vivo at the micro-scale, opening new vistas in coral biology.

Modeling reaction–diffusion processes within catalyst washcoats: I. Microscale processes based on three-dimensional reconstructions

This paper develops a detailed analysis of reaction–diffusion processes within a porous rhodium-alumina catalyst washcoat. Focused-ion-beam–scanning-electron-microscope (FIB–SEM) techniques are developed and applied to reconstruct the actual catalyst-support microstructure. Three-dimensional transport processes within washcoat micro-pore structures are modeled using a dimensionless representation of reaction and diffusion rates based on the Damköhler number. Three-dimensional computational solutions for particular porous microstructures are modeled and interpreted. In a companion paper, these microstructural results are used to assist development of larger-scale models that can be incorporated into reactor-scale simulations.

Full-Scale Spectrum of Boundary-Layer Winds

Extensive mean meteorological data and high frequency sonic anemometer data from two sites in Denmark, one coastal onshore and one offshore, have been used to study the full-scale spectrum of boundary-layer winds, over frequencies f from about $$1\,\hbox {yr}^{-1}$$ to 10 Hz. 10-min cup anemometer data are used to estimate the spectrum from about $$1\,\hbox {yr}^{-1}$$ to $$0.05\,\hbox {min}^{-1}$$ ; in addition, using 20-Hz sonic anemometer data, an ensemble of 1-day spectra covering the range $$1\,\hbox {day}^{-1}$$ to 10 Hz has been calculated. The overlapping region in these two measured spectra is in good agreement. Classical topics regarding the various spectral ranges, including the spectral gap, are revisited. Following the seasonal peak at $$1\,\hbox {yr}^{-1}$$ , the frequency spectrum fS(f) increases with $$f^{+1}$$ and gradually reaches a peak at about $$0.2\,\hbox {day}^{-1}$$ . From this peak to about $$1\,\hbox {hr}^{-1}$$ , the spectrum fS(f) decreases with frequency with a $$-2$$ slope, followed by a $$-2/3$$ slope, which can be described by $$fS(f)=a_1f^{-2/3}+a_2f^{-2}$$ , ending in the frequency range for which the debate on the spectral gap is ongoing. It is shown here that the spectral gap exists and can be modelled. The linear composition of the horizontal wind variation from the mesoscale and microscale gives the observed spectrum in the gap range, leading to a suggestion that mesoscale and microscale processes are uncorrelated. Depending on the relative strength of the two processes, the gap may be deep or shallow, visible or invisible. Generally, the depth of the gap decreases with height. In the low frequency region of the gap, the mesoscale spectrum shows a two-dimensional isotropic nature; in the high frequency region, the classical three-dimensional boundary-layer turbulence is evident. We also provide the cospectrum of the horizontal and vertical components, and the power spectra of the three velocity components over a wide range from $$1\,\hbox {day}^{-1}$$ to 10 Hz, which is useful in determining the necessary sample duration when measuring turbulence statistics in the boundary layer.

Assembly and phase transitions of colloidal crystals

Micrometre sized colloidal particles can be viewed as large atoms with tailorable size, shape and interactions. These building blocks can assemble into extremely rich structures and phases, in which the thermal motions of particles can be directly imaged and tracked using optical microscopy. Hence, colloidal particles are excellent model systems for studying phase transitions, especially for poorly understood kinetic and nonequilibrium microscale processes. Advances in colloid fabrication, assembly and computer simulations have opened up numerous possibilities for such research. In this Review, we describe recent progress in the study of colloidal crystals composed of tunable isotropic spheres, anisotropic particles and active particles. We focus on advances in crystallization, melting and solid solid transitions, and highlight challenges and future perspectives in phase transition studies within colloidal crystals.

Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities.

Studies of protein phenotypes represent a central challenge of modern genetics in the post-genome era because effective and accurate investigation of protein phenotypes is one of the most critical procedures to identify functional biological processes in microscale, which involves the analysis of multifactorial traits and has greatly contributed to the development of modern biology in the post genome era. Therefore, we have developed a novel computational method that identifies novel proteins associated with certain phenotypes in yeast based on the protein-protein interaction network. Unlike some existing network-based computational methods that identify the phenotype of a query protein based on its direct neighbors in the local network, the proposed method identifies novel candidate proteins for a certain phenotype by considering all annotated proteins with this phenotype on the global network using a shortest path (SP) algorithm. The identified proteins are further filtered using both a permutation test and their interactions and sequence similarities to annotated proteins. We compared our method with another widely used method called random walk with restart (RWR). The biological functions of proteins for each phenotype identified by our SP method and the RWR method were analyzed and compared. The results confirmed a large proportion of our novel protein phenotype annotation, and the RWR method showed a higher false positive rate than the SP method. Our method is equally effective for the prediction of proteins involving in all the eleven clustered yeast phenotypes with a quite low false positive rate. Considering the universality and generalizability of our supporting materials and computing strategies, our method can further be applied to study other organisms and the new functions we predicted can provide pertinent instructions for the further experimental verifications.

Building Consistent Multi-temporal Population Data at Fine Resolution through Spatially Refined Areal Interpolation

GIScience 2016 Short Paper Proceedings Building Consistent Multi-temporal Population Data at Fine Resolution through Spatially Refined Areal Interpolation H. Zoraghein 1 , S. Leyk 1 Department of Geography, University of Colorado Boulder, CO, 80309, USA Email: {hamidreza.zoraghein; stefan.leyk}@colorado.edu Abstract Demographic data are aggregated over areal units to protect privacy and are often inconsistent over time. Areal interpolation methods are used to estimate population in one census year within the units of another year to construct temporally consistent small census units. This research enhances these methods by using three advanced spatial refinement approaches, tested in Mecklenburg County, North Carolina to estimate population in 2000 within census tracts from the 2010 census. The results demonstrate the effectiveness of spatial refinement in reducing estimation errors, systematically. The proposed methods can be used to analyze micro-scale spatio-temporal demographic processes with minimum estimation error. 1. Introduction Spatial analysis on demographic data aggregated over incompatible boundaries represents a challenge, particularly when the data were collected over historical inconsistent units. To understand micro-scale spatio-temporal demographic processes, data need to be collected over temporally consistent fine-resolution census geographies such as census tracts. However, in reality, their boundaries change over time due to population fluctuations, especially in rapidly growing areas. Areal interpolation transfers the variable of interest from source zones to target zones and is used in temporal demographic applications (Gregory 2002; Schroeder 2007). In such applications, source populations in one census year (enumerated in source zones) are estimated within enumeration units from the target census completed in another year (target zones). If the underlying assumptions of areal interpolation methods are not met, accuracy can be very low. Therefore, recent studies have developed spatially refined interpolation techniques with the objective of decreasing population estimation errors (Buttenfield et al. 2015; Ruther et al. 2015). Areal interpolation methods are based on population density and area calculations. It can be expected that if these methods are constrained to spatially refined inhabited sub-areas of source and target zones, area and population density estimates will be more precise and realistic. Commonly, the spatially refined sub-areas are delineated using ancillary variables presumably related to population distribution in a dasymetric mapping approach (e.g., Mennis 2003). This research extends the previous efforts, leveraging three advanced spatial refinement strategies to estimate total population enumerated in census tracts in 2000 within census tract boundaries used in the 2010 census. 2. Study Area and Data The study area spans Mecklenburg County, North Carolina. It includes both urban areas of Charlotte at its center and large rural areas at its margins and has a history of rapid population growth.