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1
Sakout, Sofia, Daniel Weisz-Patrault, and Alain Ehrlacher. "Energetic upscaling strategy for grain growth. i: Fast mesoscopic model based on dissipation." Acta Materialia 196 (September 2020): 261–79. http://dx.doi.org/10.1016/j.actamat.2020.06.032.
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Zhou, Xuesong, Jeffrey Taylor, and Filippo Pratico. "DTALite: A queue-based mesoscopic traffic simulator for fast model evaluation and calibration." Cogent Engineering 1, no. 1 (October 1, 2014): 961345. http://dx.doi.org/10.1080/23311916.2014.961345.
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Wang, Enjiang, José M. Carcione, and Jing Ba. "Wave simulation in double-porosity media based on the Biot-Rayleigh theory." GEOPHYSICS 84, no. 4 (July 1, 2019): WA11—WA21. http://dx.doi.org/10.1190/geo2018-0575.1.
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We have developed a numerical algorithm for simulation of wave propagation in double-porosity media, where the pore space is saturated with a single fluid. Spherical inclusions embedded in a background medium oscillate to yield attenuation by mode conversion from fast P-wave energy to slow P-wave energy (mesoscopic or wave-induced fluid-flow loss). The theory is based on the Biot theory of poroelasticity and the Rayleigh model of bubble oscillations. The differential equation of the Biot-Rayleigh variable is approximated with the Zener mechanical model, which results in a memory-variable viscoelastic equation. These approximations are required to model mesoscopic losses arising from conversion of the fast P-wave energy to slow diffusive modes. The model predicts a relaxation peak in the seismic band, depending on the diameter of the patches, to model the attenuation level observed in rocks. The wavefield is obtained with a grid method based on the Fourier differential operator and a second-order time-integration algorithm. Because the presence of two slow quasistatic modes makes the differential equations stiff, a time-splitting integration algorithm is used to solve the stiff part analytically. The modeling has spectral accuracy in the calculation of the spatial derivatives.
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Needell, Zachary A., and Jessika E. Trancik. "Efficiently Simulating Personal Vehicle Energy Consumption in Mesoscopic Transport Models." Transportation Research Record: Journal of the Transportation Research Board 2672, no. 25 (November 20, 2018): 163–73. http://dx.doi.org/10.1177/0361198118798244.
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Mesoscopic transport models can efficiently simulate complex travel behavior and traffic patterns over large networks, but simulating energy consumption in these models is difficult with traditional methods. As mesoscopic transport models rely on a simplified handling of traffic flow, they cannot provide the second-by-second measurement of vehicle speeds and accelerations that are required for accurately estimating energy consumption. Here we present extensions to the TripEnergy model that fill in the gaps of low-resolution trajectories with realistic, contextual driving behavior. TripEnergy also includes a vehicle energy model capable of simulating the impact of traffic conditions on energy consumption and CO2 emissions, with inputs in the form of widely available calibration data, allowing it to simulate thousands of different real-world vehicle makes and models. This design allows TripEnergy to integrate with mesoscopic transport models and to be fast enough to run on a large network with minimal additional computation time. We expect it to benefit from and enable advances in transport simulation, including optimizing traffic network controls to minimize energy, evaluating the performance of different vehicle technologies under wide-scale adoption, and better understanding the energy and climate impacts of new infrastructure and policies.
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Li, Zilong, and Yang Tang. "Mesoscopic Simulation Method for Uniaxial Compression Test of RCC Dam Material Based on DEM." Mathematical Problems in Engineering 2020 (December 17, 2020): 1–13. http://dx.doi.org/10.1155/2020/6686609.
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The roller compacted concrete (RCC) dam has become one of the most competitive dam types due to its fast construction speed, low cost, and strong adaptability. However, the macroscale compaction test can hardly reflect the mesoscopic structure on the RCC’s rolling characteristics. According to the characteristics of RCC dam materials, a numerical discrete element method (DEM) is proposed in this paper, which is used to simulate the irregular shape and proportion of RCC aggregates. Moreover, a mesoscopic parameter inversion method based on the adaptive differential evolution (ADE) algorithm is proposed to enhance the efficiency of model contact parameters determination and overcome the inconvenience and time-consumption of conventional methods. Compared with the physical test, the simulation compression curve has good consistency with the physical test curve, and the proposed method can adequately reflect the physical and mechanical properties of RCC dam materials, which provides a basis for the subsequent research on the properties of RCC dam materials under different filling times.
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Biscarini, Chiara, Silvia Di Francesco, Fernando Nardi, and Piergiorgio Manciola. "Detailed Simulation of Complex Hydraulic Problems with Macroscopic and Mesoscopic Mathematical Methods." Mathematical Problems in Engineering 2013 (2013): 1–14. http://dx.doi.org/10.1155/2013/928309.
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The numerical simulation of fast-moving fronts originating from dam or levee breaches is a challenging task for small scale engineering projects. In this work, the use of fully three-dimensional Navier-Stokes (NS) equations and lattice Boltzmann method (LBM) is proposed for testing the validity of, respectively, macroscopic and mesoscopic mathematical models. Macroscopic simulations are performed employing an open-source computational fluid dynamics (CFD) code that solves the NS combined with the volume of fluid (VOF) multiphase method to represent free-surface flows. The mesoscopic model is a front-tracking experimental variant of the LBM. In the proposed LBM the air-gas interface is represented as a surface with zero thickness that handles the passage of the density field from the light to the dense phase and vice versa. A single set of LBM equations represents the liquid phase, while the free surface is characterized by an additional variable, the liquid volume fraction. Case studies show advantages and disadvantages of the proposed LBM and NS with specific regard to the computational efficiency and accuracy in dealing with the simulation of flows through complex geometries. In particular, the validation of the model application is developed by simulating the flow propagating through a synthetic urban setting and comparing results with analytical and experimental laboratory measurements.
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Zhao, Liang, Chang-Hua Li, Fa-Ning Dang, Chu-Jun Li, and Zhong-Xing Duan. "Concrete CT Image Quick Three-Dimensional Reconstruction Research." International Journal of Pattern Recognition and Artificial Intelligence 31, no. 10 (March 16, 2017): 1757005. http://dx.doi.org/10.1142/s0218001417570051.
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The research of the mechanical properties of concrete, a kind of heterogeneous composite material, was previously established on basis of the mathematical model of random aggregate, which is used to study and analyze the mesoscopic damage mechanism of concrete. Although the shape and distribution of aggregate in the model built by this method are closer to the real structure of concrete, there is still a big difference between them and the real concrete specimen. In order to solve the problem of large amount of redundant computation in the CT reconstruction of full size cube space, a fast reconstruction method based on ray-casting algorithm is proposed. First, a method integrating the new bounding box technology with the plane intersection algorithm clusters were adopted to cut the body data and ray-casting effectively, and then, the polygon scanning and conversion was utilized to reduce the number of cast rays, finally, the adaptive sampling method was used to avoid repeatedly sampling same voxel so that the reconstruction efficiency of whole algorithm and the feasibility of numerical calculation can be enhanced. The experimental results demonstrate that the proposed algorithm can greatly improve the 3D rendering speed of concrete CT without affecting the image quality. It provides a more effective and reliable approach for correctly analyzing the mesoscopic damage mechanism and mechanical characteristics of concrete.
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Koltcov, Sergei, Vera Ignatenko, and Sergei Pashakhin. "Fast Tuning of Topic Models: An Application of Rényi Entropy and Renormalization Theory." Proceedings 46, no. 1 (November 17, 2019): 5. http://dx.doi.org/10.3390/ecea-5-06674.
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In practice, the critical step in building machine learning models of big data (BD) is costly in terms of time and the computing resources procedure of parameter tuning with a grid search. Due to the size, BD are comparable to mesoscopic physical systems. Hence, methods of statistical physics could be applied to BD. The paper shows that topic modeling demonstrates self-similar behavior under the condition of a varying number of clusters. Such behavior allows using a renormalization technique. The combination of a renormalization procedure with the Rényi entropy approach allows for fast searching of the optimal number of clusters. In this paper, the renormalization procedure is developed for the Latent Dirichlet Allocation (LDA) model with a variational Expectation-Maximization algorithm. The experiments were conducted on two document collections with a known number of clusters in two languages. The paper presents results for three versions of the renormalization procedure: (1) a renormalization with the random merging of clusters, (2) a renormalization based on minimal values of Kullback–Leibler divergence and (3) a renormalization with merging clusters with minimal values of Rényi entropy. The paper shows that the renormalization procedure allows finding the optimal number of topics 26 times faster than grid search without significant loss of quality.
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Guo, Yutai, Jialong He, Hui Jiang, Yuande Zhou, Feng Jin, and Chongmin Song. "A Simple Approach for Generating Random Aggregate Model of Concrete Based on Laguerre Tessellation and Its Application Analyses." Materials 13, no. 17 (September 3, 2020): 3896. http://dx.doi.org/10.3390/ma13173896.
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Generating random aggregate models (RAMs) plays a key role in the mesoscopic modelling of concrete-like composite materials. The arbitrary geometry, wide gradation, and high volume ratio of aggregates pose a great challenge for fast and efficient numerical construction of concrete meso-structures. This paper presents a simple strategy for generating RAMs of concrete based on Laguerre tessellation, which mainly consists of three steps: tessellation, geometric smoothing, and scaling. The computer-assisted design (CAD) file of RAMs obtained by the proposed approach can be directly adopted for the construction of random numerical concrete samples. Combined with the image-based octree meshing algorithm, the scaled boundary finite element method (SBFEM) was adopted for an automatic stress analysis of mass concrete samples, and a parametric study was conducted to investigate the meso-structural effects on concrete elasticity properties. The modelling results successfully reproduced the increasing trend of concrete elastic modulus with the grading of coarse aggregates in literature test data and demonstrate the effectiveness of the proposed strategy.
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Köksal Ersöz, Elif, Julien Modolo, Fabrice Bartolomei, and Fabrice Wendling. "Neural mass modeling of slow-fast dynamics of seizure initiation and abortion." PLOS Computational Biology 16, no. 11 (November 9, 2020): e1008430. http://dx.doi.org/10.1371/journal.pcbi.1008430.
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Epilepsy is a dynamic and complex neurological disease affecting about 1% of the worldwide population, among which 30% of the patients are drug-resistant. Epilepsy is characterized by recurrent episodes of paroxysmal neural discharges (the so-called seizures), which manifest themselves through a large-amplitude rhythmic activity observed in depth-EEG recordings, in particular in local field potentials (LFPs). The signature characterizing the transition to seizures involves complex oscillatory patterns, which could serve as a marker to prevent seizure initiation by triggering appropriate therapeutic neurostimulation methods. To investigate such protocols, neurophysiological lumped-parameter models at the mesoscopic scale, namely neural mass models, are powerful tools that not only mimic the LFP signals but also give insights on the neural mechanisms related to different stages of seizures. Here, we analyze the multiple time-scale dynamics of a neural mass model and explain the underlying structure of the complex oscillations observed before seizure initiation. We investigate population-specific effects of the stimulation and the dependence of stimulation parameters on synaptic timescales. In particular, we show that intermediate stimulation frequencies (>20 Hz) can abort seizures if the timescale difference is pronounced. Those results have the potential in the design of therapeutic brain stimulation protocols based on the neurophysiological properties of tissue.
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Zhu, Shi Sha, Tao Tang, Xin Zi Tang, Jin Gang Liu, Xue Peng Qian, and Hao He. "Dynamic Modeling and Numerical Simulation of Electrorheological Fluids Based on Lattice Boltzmann Method." Applied Mechanics and Materials 487 (January 2014): 494–99. http://dx.doi.org/10.4028/www.scientific.net/amm.487.494.
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Since the fast response of the internal structure of the Electrorheological (ER) suspension fluids occurs in the controlled space (electrode distance is generally 1-2 mm) of the applied electric field, where the main feature of the ER suspension fluids in the certain time and spatial scales is low shear rate but high flow resistance, which means the Mach number and the Reynolds number are generally small, it can be researched as micro-scale flow. According to this characteristic, the author proposed a discrete-particle-motion model of the ER suspension flows based on the Lattice Boltzmann method(LBM) of the Mesoscopic kinetic theory. The results of the dynamic simulation showed that the model solved the problem of describing the changes of the rheological properties of some local flow fields and the influences on the particle movement during the two-way coupling in this flow field.
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Zhu, Wen, and Zehua Zhang. "Calibration Method of Normal Critical Damping Ratio in Particle Discrete Element Rock Model." Advances in Engineering Technology Research 1, no. 2 (September 24, 2022): 514. http://dx.doi.org/10.56028/aetr.1.2.514.
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The calibration of dynamic mesoscopic parameters such as the normal critical damping ratio will directly affect the simulation results when wave velocity dynamic analysis is carried out on the particle discrete element rock model. This paper presents a fast calibration method for the normal critical damping ratio in the particle discrete element model. Firstly, the relationship between the normal critical damping ratio and the model energy attenuation rate is quantitatively analyzed based on the fundamental theory of discrete particle elements and energy conservation law. Then, based on the rock model with determined macroscopic mechanical parameters, the elastic longitudinal wave test is carried out to study the influence of the model energy attenuation rate with a normal critical damping ratio. The theoretical formula is modified according to the numerical results. Finally, the calibration formula of the normal critical damping ratio in the discrete particle element model is given. It is a new method to calibrate the normal critical damping ratio of the discrete particle model quickly and conveniently by using the theory of discrete particle elements and energy. It can provide a reference for constructing an accurate particle discrete element rock model.
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Zhu, Wen, and Zehua Zhang. "Calibration Method of Normal Critical Damping Ratio in Particle Discrete Element Rock Model." Advances in Engineering Technology Research 2, no. 1 (September 24, 2022): 514. http://dx.doi.org/10.56028/aetr.2.1.514.
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The calibration of dynamic mesoscopic parameters such as the normal critical damping ratio will directly affect the simulation results when wave velocity dynamic analysis is carried out on the particle discrete element rock model. This paper presents a fast calibration method for the normal critical damping ratio in the particle discrete element model. Firstly, the relationship between the normal critical damping ratio and the model energy attenuation rate is quantitatively analyzed based on the fundamental theory of discrete particle elements and energy conservation law. Then, based on the rock model with determined macroscopic mechanical parameters, the elastic longitudinal wave test is carried out to study the influence of the model energy attenuation rate with a normal critical damping ratio. The theoretical formula is modified according to the numerical results. Finally, the calibration formula of the normal critical damping ratio in the discrete particle element model is given. It is a new method to calibrate the normal critical damping ratio of the discrete particle model quickly and conveniently by using the theory of discrete particle elements and energy. It can provide a reference for constructing an accurate particle discrete element rock model.
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Picotti, Stefano, José M. Carcione, and Mauro Pavan. "Seismic attenuation in Antarctic firn." Cryosphere 18, no. 1 (January 9, 2024): 169–86. http://dx.doi.org/10.5194/tc-18-169-2024.
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Abstract. We estimate the seismic attenuation of P and S waves in the polar firn and underlying ice by spectral analysis of diving, refracted, and reflected waves from active-source three-component seismic signals obtained in 2010 on the Whillans Ice Stream (WIS), a fast-flowing ice stream in West Antarctica. The resulting quality factors are then successfully modeled using a rock-physics theory of wave propagation that combines White's mesoscopic attenuation theory of interlayer flow with that of Biot/squirt flow. The first theory describes an equivalent viscoelastic medium consisting of a stack of two alternating thin porous layers, both of which have thicknesses that are much greater than the pore size but smaller than the wavelength. On the other hand, in the so-called Biot/squirt-flow model, there are two loss mechanisms, namely the global Biot flow and the local flow from fluid-filled microcracks (or grain contacts) to the pore space and back, where the former is dominant over the latter. The fluid saturating the pores is assumed to be fluidized snow, defined as a mixture of snow particles and air, such as powder, with a rigidity modulus of zero.
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Saroji, Sudarmaji, Budi Eka Nurcahya, and Nivan Ramadhan Sugiantoro. "Vertical to Horizontal Spectral Ratio (VHSR) Response of Seismic Wave Propagation in a Homogeneous Elastic – Poroelastic Medium Using The Spectral Finite Element Method." INDONESIAN JOURNAL OF APPLIED PHYSICS 11, no. 1 (April 30, 2021): 95. http://dx.doi.org/10.13057/ijap.v11i1.45969.
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<p>Numerical modeling of 2D seismic wave propagation using spectral finite element method to estimate the response of seismic waves passing through the poroelastic medium from a hydrocarbon reservoir has been carried out. A hybrid simple model of the elastic - poroelastic - elastic with a mesoscopic scale element size of about 50cm was created. Seismic waves which was in the form of the ricker function are generated on the first elastic medium, propagated into the poroelastic medium and then transmitted to the second elastic medium. Pororoelastic medium is bearing hydrocarbon fluid in the form of gas, oil or water. Vertical and horizontal component of velocity seismograms are recorded on all mediums. Seismograms which are recorded in the poroelastic and second elastic medium show the existence of slow P compressional waves following fast P compressional waves that do not appear on the seismogram of the first elastic medium. The slow P wave is generated when the fast P wave enters the interface of the elastic - poroelastic boundary, propagated in the poroelastic medium and is transmited to the second elastic medium. The curves of Vertical to horizontal spectrum ratio (VHSR) which are observed from seismograms recorded in the poroelastic and the second elastic medium show that the peak of VHSR values at low frequency correlated with the fluid of poroelastic reservoir. The highest VHSR value at the low frequency which is recorded on the seismogram is above the 2.5 Hz frequency for reservoirs containing gas and oil in the second elastic medium, while for the medium containing water is the highest VHSR value is below the 2.5 Hz frequency.</p>
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Aqil, Marco, Selen Atasoy, Morten L. Kringelbach, and Rikkert Hindriks. "Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome." PLOS Computational Biology 17, no. 1 (January 28, 2021): e1008310. http://dx.doi.org/10.1371/journal.pcbi.1008310.
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Tools from the field of graph signal processing, in particular the graph Laplacian operator, have recently been successfully applied to the investigation of structure-function relationships in the human brain. The eigenvectors of the human connectome graph Laplacian, dubbed “connectome harmonics”, have been shown to relate to the functionally relevant resting-state networks. Whole-brain modelling of brain activity combines structural connectivity with local dynamical models to provide insight into the large-scale functional organization of the human brain. In this study, we employ the graph Laplacian and its properties to define and implement a large class of neural activity models directly on the human connectome. These models, consisting of systems of stochastic integrodifferential equations on graphs, are dubbed graph neural fields, in analogy with the well-established continuous neural fields. We obtain analytic predictions for harmonic and temporal power spectra, as well as functional connectivity and coherence matrices, of graph neural fields, with a technique dubbed CHAOSS (shorthand for Connectome-Harmonic Analysis Of Spatiotemporal Spectra). Combining graph neural fields with appropriate observation models allows for estimating model parameters from experimental data as obtained from electroencephalography (EEG), magnetoencephalography (MEG), or functional magnetic resonance imaging (fMRI). As an example application, we study a stochastic Wilson-Cowan graph neural field model on a high-resolution connectome graph constructed from diffusion tensor imaging (DTI) and structural MRI data. We show that the model equilibrium fluctuations can reproduce the empirically observed harmonic power spectrum of resting-state fMRI data, and predict its functional connectivity, with a high level of detail. Graph neural fields natively allow the inclusion of important features of cortical anatomy and fast computations of observable quantities for comparison with multimodal empirical data. They thus appear particularly suitable for modelling whole-brain activity at mesoscopic scales, and opening new potential avenues for connectome-graph-based investigations of structure-function relationships.
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Picotti, Stefano, José M. Carcione, and Jing Ba. "Rock-physics templates based on seismic Q." GEOPHYSICS 84, no. 1 (January 1, 2019): MR13—MR23. http://dx.doi.org/10.1190/geo2018-0017.1.
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We build rock-physics templates (RPTs) for reservoir rocks based on seismic quality factors. In these templates, the effects of partial saturation, porosity, and permeability on the seismic properties are described by generalizing the Johnson mesoscopic-loss model to a distribution of gas-patch sizes in brine- and oil-saturated rocks. This model addresses the wave-induced fluid flow attenuation mechanism, by which part of the energy of the fast P-wave is converted into the slow P (Biot) diffusive mode. We consider patch sizes, whose probability density function is defined by a normal (Gaussian) distribution. The complex bulk modulus of the composite medium is obtained with the Voigt-Reuss-Hill average, and we show that the results are close to those obtained with the Hashin-Shtrikman average. The templates represent the seismic dissipation factor (reciprocal of seismic quality factor) as a function of the P-wave velocity, acoustic impedance, and [Formula: see text] (P to S velocity ratio), for isolines of saturation, porosity, and permeability. They differentiate between oil and brine on the basis of the quality factor, with the gas-brine case showing more dissipation than the gas-oil case. We obtain sensitivity maps of the seismic properties to gas saturation and porosity for brine and oil. Unlike the gas-brine case, which shows higher sensitivity of attenuation to gas saturation, the gas-oil case shows higher sensitivity to porosity, and higher acoustic impedance and [Formula: see text] sensitivity values versus saturation. The RPTs can be used for a robust sensitivity analysis, which provides insights on seismic attributes for hydrocarbon detection and reservoir delineation. The templates are also relevant for studies related to [Formula: see text]-storage monitoring.
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Fritsch, Anatol W., Andrés F. Diaz-Delgadillo, Omar Adame-Arana, Carsten Hoege, Matthäus Mittasch, Moritz Kreysing, Mark Leaver, Anthony A. Hyman, Frank Jülicher, and Christoph A. Weber. "Local thermodynamics govern formation and dissolution of Caenorhabditis elegans P granule condensates." Proceedings of the National Academy of Sciences 118, no. 37 (September 10, 2021): e2102772118. http://dx.doi.org/10.1073/pnas.2102772118.
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Membraneless compartments, also known as condensates, provide chemically distinct environments and thus spatially organize the cell. A well-studied example of condensates is P granules in the roundworm Caenorhabditis elegans that play an important role in the development of the germline. P granules are RNA-rich protein condensates that share the key properties of liquid droplets such as a spherical shape, the ability to fuse, and fast diffusion of their molecular components. An outstanding question is to what extent phase separation at thermodynamic equilibrium is appropriate to describe the formation of condensates in an active cellular environment. To address this question, we investigate the response of P granule condensates in living cells to temperature changes. We observe that P granules dissolve upon increasing the temperature and recondense upon lowering the temperature in a reversible manner. Strikingly, this temperature response can be captured by in vivo phase diagrams that are well described by a Flory–Huggins model at thermodynamic equilibrium. This finding is surprising due to active processes in a living cell. To address the impact of such active processes on intracellular phase separation, we discuss temperature heterogeneities. We show that, for typical estimates of the density of active processes, temperature represents a well-defined variable and that mesoscopic volume elements are at local thermodynamic equilibrium. Our findings provide strong evidence that P granule assembly and disassembly are governed by phase separation based on local thermal equilibria where the nonequilibrium nature of the cytoplasm is manifested on larger scales.
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Cramer, Samuel, Laurentiu Popa, Samuel Haley, Sanjay Dhawan, Russell Carter, Jianfang Ning, Justin Aronson, Suhasa Kodandaramaiah, Timothy Ebner, and Clark Chen. "PATH-02. CHARACTERIZATION OF FUNCTIONAL NETWORK EFFECTS IN THE CEREBRAL CORTEX DURING BRAIN TUMORIGENESIS IN THE MOUSE." Neuro-Oncology 22, Supplement_2 (November 2020): ii164. http://dx.doi.org/10.1093/neuonc/noaa215.684.
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Abstract INTRODUCTION Neuro-cognitive decline is near universal in glioblastoma patients and negatively impacts the quality of life for afflicted patients. Yet, there is little information on longitudinal effects of brain tumor growth on cerebral cortical function and network connectivity. OBJECTIVE To address this knowledge gap, we examined in vivo Ca2+ flux imaging in a transgenic murine glioblastoma model. METHODS Mesoscopic Ca2+ imaging was performed after implant of GL261 glioblastoma cells into a transgenic mice strain (Thy1-GCaMP6f) that expresses the fast calcium indicator GCaMP6f in Layer II/III and Layer V pyramidal neurons. Independent component analysis (ICA), correlation matrix and graph theory approaches were used to assess changes in network connectivity. RESULTS ICA defined canonical cerebral network consisting of nodal convergence and connectivity between nodes. The overall network structure remained unaltered after tumor implant. A decrease in the strength of connectivity was observed immediately following tumor implant. This temporary suppression was followed by progressive, global increase in the strength of nodal connectivity (p < 0.0001). By two weeks post-tumor implant, 50% of the nodes exhibited increased connectivity compared to baseline. Progressive activation of select nodes was also observed in the weeks following tumor implant (p < 0.01). In aggregate, these results suggest that activation of select network nodes as well as enhanced connectivity as means to compensate for the deleterious effects of glioblastoma growth. CONCLUSIONS Our results indicate that focal brain tumor growth induces a reorganization of both local and remote cortical activity. The finding bear pertinence to the pathogenesis of neuro-cognitive decline and tumor associated epilepsy.
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Cramer, Samuel, Laurentiu Popa, Samuel Haley, Sanjay Dhawan, Russell Carter, Jianfang Ning, Justin Aronson, Suhasa Kodandaramaiah, Timothy Ebner, and Clark Chen. "TMOD-10. EFFECT OF BRAIN TUMORIGENESIS ON CEREBRAL CORTICAL FUNCTIONAL CONNECTIVITY IN THE MOUSE." Neuro-Oncology 22, Supplement_2 (November 2020): ii229—ii230. http://dx.doi.org/10.1093/neuonc/noaa215.961.
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Abstract INTRODUCTION Neuro-cognitive decline is near universal in glioblastoma patients and negatively impacts the quality of life for afflicted patients. Yet, there is little information on longitudinal effects of brain tumor growth on cerebral cortical function and network connectivity. OBJECTIVE To address this knowledge gap, we examined in vivo Ca2+ imaging in a transgenic murine glioblastoma model. METHODS Mesoscopic Ca2+ imaging was performed after implant of GL261 glioblastoma cells into a transgenic mice strain (Thy1-GCaMP6f) that expresses the fast calcium indicator GCaMP6f in Layer II/III and Layer V pyramidal neurons. Independent component analysis (ICA), correlation matrix and graph theory approaches were used to assess changes in network connectivity. RESULTS ICA defined canonical cerebral network consisting of nodal convergence and connectivity between nodes. The overall network structure remained unaltered after tumor implant. A decrease in the strength of connectivity was observed immediately following tumor implant. This temporary suppression was followed by progressive, global increase in the strength of nodal connectivity (p < 0.0001). By two weeks post-tumor implant, 50% of the nodes exhibited increased connectivity compared to baseline. Progressive activation of select nodes was also observed in the weeks following tumor implant (p < 0.01). In aggregate, these results suggest that activation of select network nodes as well as enhanced connectivity as means to compensate for the deleterious effects of glioblastoma growth. CONCLUSIONS Our results indicate that focal brain tumor growth induces a reorganization of both local and remote cortical activity. The finding bears pertinence to the pathogenesis of neuro-cognitive decline and tumor-associated epilepsy.
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SUÑE, JORDI, DAVID JIMENEZ, and ENRIQUE MIRANDA. "BREAKDOWN MODES AND BREAKDOWN STATISTICS OF ULTRATHIN SiO2 GATE OXIDES." International Journal of High Speed Electronics and Systems 11, no. 03 (September 2001): 789–848. http://dx.doi.org/10.1142/s0129156401001003.
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The dielectric breakdown of ultra-thin silicon dioxide films used as gate insulator in MOSFETs is one of the most important reliability issues in CMOS technology. In this paper, two main aspects of oxide breakdown are considered: the modeling of the breakdown statistics and the properties of the two main breakdown modes, namely Soft Breakdown and Hard Breakdown. The most invoked models for the breakdown statistics that relate defect generation and breakdown are reviewed. Particular attention is paid to the percolation models and to a recent cell-based analytic picture. The scaling of the breakdown distribution with oxide thickness is considered and it is shown that both pictures are equivalent for ultra-thin oxides. It is shown that soft and hard breakdown show coincident statistics and this is used to conclude that both breakdown models are triggered by the formation of the same kind of defect-related conduction paths. The big differences in the post-breakdown conduction properties are attributed to phenomena occurring during the very fast breakdown current runaway that determine the area of the final breakdown spot. The properties of soft and hard breakdown are explained within the common framework of a model based on quantum-point-contact conduction. This mesoscopic approach to the post-breakdown conduction is shown to explain the main experimental results including conductance quantization after hard breakdown, the area and thickness independence of the soft-breakdown I(V) characteristics and the statistical correlation between current level and normalized conductance. Finally, we deal with some open questions and relevant issues that are now subject of intensive investigations. The fact that some breakdown events can be tolerated for some digital applications is considered. In this regard, the distinction between breakdown and device failure distributions is made and some implications for device reliability are discussed. It is argued that energy dissipation during the breakdown runaway can determine the breakdown efficiency, the prevalence ratio of soft to hard breakdown, and their variations with stress conditions, experimental setup (series impedance) and sample characteristics.
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Miller, RJ Dwayne. "2000 John C. Polanyi Award LectureMother Nature and the molecular Big Bang." Canadian Journal of Chemistry 80, no. 1 (January 1, 2002): 1–24. http://dx.doi.org/10.1139/v01-199.
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Biological molecules are mesoscopic systems that bridge the quantum and classical worlds. At the single molecule level, there are often more than 1 × 104 degrees of freedom that are involved in protein-mediated processes. These molecules are sufficiently large that the bath coordinate convolved to the reaction at an active site is defined by the surrounding protein tertiary structure. In this context, the very interatomic forces that determine the active protein structures create a strongly associated system. Thus, the bath fluctuations leading to reactive crossings involve highly hindered motions within a myriad of local minima that would act to cast the reaction dynamics into the high viscosity limit appropriate to glasses. However, the time scales observed for biological events are orders of magnitude too fast to meet this anticipated categorization. In this context, the apparent deterministic nature of biological processes represents an enormous challenge to our understanding of chemical processes. Somehow Nature has discovered a molecular scaffolding that enables minute amounts of energy to be efficiently channeled to perform biological functions without becoming entrapped in local minima. Clearly, energy derived from chemical processes is highly directed in biological systems. To understand this problem, we must first understand how energy is redistributed among the different degrees of freedom and fully characterize the protein relaxation processes along representative reaction coordinates in relation to these dissipative processes. This paper discusses the development of new nonlinear spectroscopic methods that have enabled interferometric sensitivity to protein motions on femtosecond time scales appropriate to the very fastest motions (i.e., bond breaking or the molecular "Big Bang") out to the slowest relaxation steps. This work has led to the Collective Mode Coupling Model as an explanation of the required reduced dimensionality in biological systems. Within this model, the largest coupling coefficients of the reaction coordinate are to the damped inertial collective modes of the protein defined by the strongly correlated secondary structures. These modes act to guide the reaction along the correct seam(s) in an otherwise highly complex potential energy surface. The mechanism by which biological molecules have been able to harness chemical energy over meso-length scales represents the first step towards higher levels of organization. The new insight afforded by the collective mode mechanism may prove important in understanding this larger issue of scaling in biological systems.Key words: biodynamics, energy transduction, ultrafast spectroscopy, nonlinear spectroscopy, primary processes in biology.
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Paulsson, Johan, and Måns Ehrenberg. "Noise in a minimal regulatory network: plasmid copy number control." Quarterly Reviews of Biophysics 34, no. 1 (February 2001): 1–59. http://dx.doi.org/10.1017/s0033583501003663.
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1. Introduction 22. Plasmid biology 32.1 What are plasmids? 32.2 Evolution of CNC: cost and benefit 42.3 Plasmids are semi-complete regulatory networks 62.4 The molecular mechanisms of CNC for plasmids ColE1 and R1 62.4.1 ColE1 72.4.2 R1 72.5 General simplifying assumptions and values of rate constants 93. Macroscopic analysis 113.1 Regulatory logic of inhibitor-dilution CNC 113.2 Sensitivity amplification 123.3 Plasmid control curves 133.4 Multistep control of plasmid ColE1: exponential control curves 143.5 Multistep control of plasmid R1: hyperbolic control curves 163.6 Time-delays, oscillations and critical damping 184. Mesoscopic analysis 204.1 The master equation approach 204.2 A random walker in a potential well 234.3 CNC as a stochastic process 244.4 Sensitivity amplification 264.4.1 Single-step hyperbolic control 264.4.2 ColE1 multistep control can eliminate plasmid copy number variation 284.4.3 Replication backup systems – the Rom protein of ColE1 and CopB of R1 294.5 Time-delays 304.5.1 Limited rate of inhibitor degradation 304.5.2 Precise delays – does unlimited sensitivity amplification always reduce plasmid losses? 324.6 Order and disorder in CNC 334.6.1 Disordered CNC 344.6.2 Ordered CNC: R1 multistep control gives narrowly distributed interreplication times 344.7 Noisy signalling – disorder and sensitivity amplification 374.7.1 Eliminating a fast but noisy variable 384.7.2 Conditional inhibitor distribution: Poisson 394.7.3 Increasing inhibitor variation I: transcription in bursts 404.7.4 Increasing inhibitor variation II: duplex formation 414.7.5 Exploiting fluctuations for sensitivity amplification: stochastic focusing 444.7.6 A kinetic uncertainty principle 454.7.7 Disorder and stochastic focusing 464.7.8 Do plasmids really use stochastic focusing? 474.8 Metabolic burdens and values of in vivo rate constants 485. Previous models of copy number control 495.1 General models of CNC 495.2 Modelling plasmid ColE1 CNC 495.3 Modelling plasmid R1 CNC 526. Summary and outlook: the plasmid paradigm 537. Acknowledgements 568. References 56This work is a theoretical analysis of random fluctuations and regulatory efficiency in genetic networks. As a model system we use inhibitor-dilution copy number control (CNC) of the bacterial plasmids ColE1 and R1. We chose these systems because they are simple and well-characterised but also because plasmids seem to be under an evolutionary pressure to reduce both average copy numbers and statistical copy number variation: internal noise.
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Riera, Jorge J., Takeshi Ogawa, Takakuni Goto, Akira Sumiyoshi, Hiroi Nonaka, Alan Evans, Hiroyoshi Miyakawa, and Ryuta Kawashima. "Pitfalls in the dipolar model for the neocortical EEG sources." Journal of Neurophysiology 108, no. 4 (August 15, 2012): 956–75. http://dx.doi.org/10.1152/jn.00098.2011.
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For about six decades, primary current sources of the electroencephalogram (EEG) have been assumed dipolar in nature. In this study, we used electrophysiological recordings from anesthetized Wistar rats undergoing repeated whisker deflections to revise the biophysical foundations of the EEG dipolar model. In a first experiment, we performed three-dimensional recordings of extracellular potentials from a large portion of the barrel field to estimate intracortical multipolar moments generated either by single spiking neurons (i.e., pyramidal cells, PC; spiny stellate cells, SS) or by populations of them while experiencing synchronized postsynaptic potentials. As expected, backpropagating spikes along PC dendrites caused dipolar field components larger in the direction perpendicular to the cortical surface (49.7 ± 22.0 nA·mm). In agreement with the fact that SS cells have “close-field” configurations, their dipolar moment at any direction was negligible. Surprisingly, monopolar field components were detectable both at the level of single units (i.e., −11.7 ± 3.4 nA for PC) and at the mesoscopic level of mixed neuronal populations receiving extended synaptic inputs within either a cortical column (−0.44 ± 0.20 μA) or a 2.5-m3-voxel volume (−3.32 ± 1.20 μA). To evaluate the relationship between the macroscopically defined EEG equivalent dipole and the mesoscopic intracortical multipolar moments, we performed concurrent recordings of high-resolution skull EEG and laminar local field potentials. From this second experiment, we estimated the time-varying EEG equivalent dipole for the entire barrel field using either a multiple dipole fitting or a distributed type of EEG inverse solution. We demonstrated that mesoscopic multipolar components are altogether absorbed by any equivalent dipole in both types of inverse solutions. We conclude that the primary current sources of the EEG in the neocortex of rodents are not precisely represented by a single equivalent dipole and that the existence of monopolar components must be also considered at the mesoscopic level.
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Qiu, Yongrong, and Guoxin Zhang. "Stress and damage in concrete induced by pipe cooling at mesoscopic scale." Advances in Mechanical Engineering 9, no. 2 (February 2017): 168781401769050. http://dx.doi.org/10.1177/1687814017690509.
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Pipe cooling is one of the most important measures of mass concrete temperature control, but pipe cooling has its advantages and disadvantages. Inappropriate pipe-cooling water temperature may result in excessive stress and crack. Considering the fact that concrete is a type of three-phase composite material and the sizes of cooling pipe and aggregate are basically on the same scale, the mesoscopic heterogeneity of concrete may have a great effect on the stress field surrounding the pipe. This article computes the pipe cooling–induced stress and damage and analyzes the differences between the homogeneous model and heterogeneous model based on mesoscopic mechanics. In this study, both linear elastic analysis and nonlinear damage analysis are performed; elastic modulus and creep are used as a function of concrete age; and several factors such as temperature difference, multistep cooling mode, and earlier cooling are also studied. The research results show that due to the mesoscopic heterogeneity characteristics of concrete, there is a great deal of difference between homogeneous model and heterogeneous model; pipe cooling can lead to large residual stress around the aggregate and produce a large range of damage, and previous homogeneous model indeed underestimates the effect of cooling-induced stress; using multistep cooling and early cooling mode can reduce this damage; the cooling-induced damage has significant influence on the anti-crack performance of concrete. In the final, based on the research results, the temperature difference between the concrete and pipe water of the second-phase cooling was recommended to be controlled at approximately 5°C.
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Bianciardi, Camilla, Alessia Allevi, and Maria Bondani. "Experimental Validation of the Statistical Properties of Speckled-Speckle Fields in the Mesoscopic Intensity Regime." Applied Sciences 13, no. 7 (April 1, 2023): 4490. http://dx.doi.org/10.3390/app13074490.
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Several imaging techniques, such as ghost imaging, are based on the use of classical and quantum correlated light states. This fact has encouraged the search for new strategies to produce light states more correlated than the thermal states that are typically used. In this work, we produce and characterize classical states of light with “more than thermal” statistics. Such states are obtained by means of a sequence of two rotating ground-glass disks and by appropriately selecting the speckle field produced at the output of each disk. The experimental results are in excellent agreement with the developed theoretical model, suggesting the potential of this kind of light for imaging applications.
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Beltz, Glenn E., and Don M. Lipkin. "A Dislocation Model for the Directional Anisotropy of Grain-Boundary Fracture." MRS Bulletin 25, no. 5 (May 2000): 21–26. http://dx.doi.org/10.1557/mrs2000.69.
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That fracture is governed by processes occurring over a wide range of length scales has been recognized since the earliest developments of modern fracture mechanics. Griffitha's study of the strength of cracked solids 1,2 is perhaps the earliest example of such multiscale thinking, predating by several decades the first attempts to apply atomistically grounded traction-separation laws to fracture (e.g., the Orowan-Gilman model3,4). Griffith recognized the critical condition for crack extension to be a statement of thermodynamic equilibrium of a cracked solid, representing a balance between the mechanical energy decrease upon crack extension and the corresponding increase in energy due to the newly created crack surface. Griffith determined the elastic strain energy of the cracked body using the continuum solution of the stress field about an ellipse5 and recognized that the potential energy associated with the cleavage surfaces of the crack was directly proportional to the surface energy, the latter deriving from the cohesive molecular forces of the solid. The Irwin-Orowan extension of Griffith mechanics to include plastic dissipation,6-9 which is known to occur on the mesoscopic length scale (~1–100 μm), provides yet a further example of multiscale thinking in the early community of fracture researchers. In fact, the interaction of length scales is of central importance in most problems of fracture.
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Schmickl, Thomas. "Strong Emergence Arising from Weak Emergence." Complexity 2022 (November 25, 2022): 1–17. http://dx.doi.org/10.1155/2022/9956885.
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Predictions of emergent phenomena, appearing on the macroscopic layer of a complex system, can fail if they are made by a microscopic model. This study demonstrates and analyses this claim on a well-known complex system, Conway’s Game of Life. Straightforward macroscopic mean-field models are easily capable of predicting such emergent properties after they have been fitted to simulation data in an after-the-fact way. Thus, these predictions are macro-to-macro only. However, a micro-to-macro model significantly fails to predict correctly, as does the obvious mesoscopic modeling approach. This suggests that some macroscopic system properties in a complex dynamic system should be interpreted as examples of phenomena (properties) arising from “strong emergence,” due to the lack of ability to build a consistent micro-to-macro model, that could explain these phenomena in a before-the-fact way. The root cause for this inability to predict this in a micro-to-macro way is identified as the pattern formation process, a phenomenon that is usually classified as being of “weak emergence.” Ultimately, this suggests that it may be in principle impossible to discriminate between such distinct categories of “weak” and “strong” emergence, as phenomena of both types can be part of the very same feedback loop that mainly governs the system’s dynamics.
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Penna, Vittorio, Alessandra Contestabile, and Andrea Richaud. "Ground-State Properties and Phase Separation of Binary Mixtures in Mesoscopic Ring Lattices." Entropy 23, no. 7 (June 28, 2021): 821. http://dx.doi.org/10.3390/e23070821.
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We investigated the spatial phase separation of the two components forming a bosonic mixture distributed in a four-well lattice with a ring geometry. We studied the ground state of this system, described by means of a binary Bose–Hubbard Hamiltonian, by implementing a well-known coherent-state picture which allowed us to find the semi-classical equations determining the distribution of boson components in the ring lattice. Their fully analytic solutions, in the limit of large boson numbers, provide the boson populations at each well as a function of the interspecies interaction and of other significant model parameters, while allowing to reconstruct the non-trivial architecture of the ground-state four-well phase diagram. The comparison with the L-well (L=2,3) phase diagrams highlights how increasing the number of wells considerably modifies the phase diagram structure and the transition mechanism from the full-mixing to the full-demixing phase controlled by the interspecies interaction. Despite the fact that the phase diagrams for L=2,3,4 share various general properties, we show that, unlike attractive binary mixtures, repulsive mixtures do not feature a transition mechanism which can be extended to an arbitrary lattice of size L.
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Oh, Simon, Ravi Seshadri, Carlos Lima Azevedo, and Moshe E. Ben-Akiva. "Demand Calibration of Multimodal Microscopic Traffic Simulation using Weighted Discrete SPSA." Transportation Research Record: Journal of the Transportation Research Board 2673, no. 5 (April 8, 2019): 503–14. http://dx.doi.org/10.1177/0361198119842107.
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This paper presents a stochastic approximation framework to solve a generalized problem of off-line calibration of demand for a multimodal microscopic (or mesoscopic) network simulation using aggregated sensor data. A key feature of this problem is that demand, although typically treated as a continuous variable is in fact discrete, particularly in the context of agent-based simulation. To address this, we first use a discrete version of the weighted simultaneous perturbation stochastic approximation (W-DSPSA) algorithm for minimizing a generalized least squares (GLS) objective (that measures the distance between simulated and observed measurements), defined over discrete sets. The algorithm computes the gradient at each iteration using a symmetric discrete perturbation of the calibration parameters and a multimodal weight matrix to improve the accuracy of the gradient estimate. The W-DSPSA algorithm is then applied to the large-scale calibration of multimodal origin–destination (OD) flows (including private vehicle (PVT) and public transit (PT) trips) in a microscopic network simulation model of Singapore. The results indicate that an acceptable margin of error on the vehicle loop count (VLC) and bus passenger count (BPC) are achieved at convergence with an improvement of 60%~80% in root mean squared errors. Lastly, we validate the calibration results with observed travel times on the network. Statistical comparison shows good agreements on both point-to-point travel time (PTT) and public buses’ stop-to-stop ride-time (SRT) with the field observations.
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Philippi, Paulo C., Keijo K. Mattila, Diogo N. Siebert, Luís O. E. dos Santos, Luiz A. Hegele Júnior, and Rodrigo Surmas. "Lattice-Boltzmann equations for describing segregation in non-ideal mixtures." Journal of Fluid Mechanics 713 (October 26, 2012): 564–87. http://dx.doi.org/10.1017/jfm.2012.473.
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AbstractIn fluid mechanics, multicomponent fluid systems are generally treated either as homogeneous solutions or as completely immiscible parts of a multiphasic system. In immiscible systems, the main task in numerical simulations is to find the location of the interface evolving over time, driven by normal and tangential surface forces. The lattice-Boltzmann method (LBM), on the other hand, is based on a mesoscopic description of the multicomponent fluid systems, and appears to be a promising framework that can lead to realistic predictions of segregation in non-ideal mixtures of partially miscible fluids. In fact, the driving forces in segregation are of a molecular nature: there is competition between the intermolecular forces and the random thermal motion of the molecules. Since these microscopic mechanisms are not accessible from a macroscopic standpoint, the LBM can provide a bridge linking the microscopic and macroscopic domains. To this end, the first purpose of this article is to present the kinetic equations in their continuum forms for the description of the mixing and segregation processes in mixtures. This paper is limited to isothermal segregation; non-isothermal segregation was discussed by Philippi et al. (Phil. Trans. R. Soc., vol. 369, 2011, pp. 2292–2300). Discretization of the kinetic equations leads to evolution equations, written in LBM variables, directly amenable for numerical simulations. Here the dynamics of the kinetic model equations is demonstrated with numerical simulations of a spinodal decomposition problem with dissolution. Finally, some simplified versions of the kinetic equations suitable for immiscible flows are discussed.
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Gorshkov, Vyacheslav N., Mykola O. Stretovych, Valerii F. Semeniuk, Mikhail P. Kruglenko, Nadiia I. Semeniuk, Victor I. Styopkin, Alexander M. Gabovich, and Gernot K. Boiger. "Hierarchical Structuring of Black Silicon Wafers by Ion-Flow-Stimulated Roughening Transition: Fundamentals and Applications for Photovoltaics." Nanomaterials 13, no. 19 (October 6, 2023): 2715. http://dx.doi.org/10.3390/nano13192715.
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Ion-flow-stimulated roughening transition is a phenomenon that may prove useful in the hierarchical structuring of nanostructures. In this work, we have investigated theoretically and experimentally the surface texturing of single-crystal and multi-crystalline silicon wafers irradiated using ion-beam flows. In contrast to previous studies, ions had relatively low energies, whereas flow densities were high enough to induce a quasi-liquid state in the upper silicon layers. The resulting surface modifications reduced the wafer light reflectance to values characteristic of black silicon, widely used in solar energetics. Features of nanostructures on different faces of silicon single crystals were studied numerically based on the mesoscopic Monte Carlo model. We established that the formation of nano-pyramids, ridges, and twisting dune-like structures is due to the stimulated roughening transition effect. The aforementioned variety of modified surface morphologies arises due to the fact that the effects of stimulated surface diffusion of atoms and re-deposition of free atoms on the wafer surface from the near-surface region are manifested to different degrees on different Si faces. It is these two factors that determine the selection of the allowable “trajectories” (evolution paths) of the thermodynamic system along which its Helmholtz free energy, F, decreases, concomitant with an increase in the surface area of the wafer and the corresponding changes in its internal energy, (), and entropy, (), so that , where is the absolute temperature. The basic theoretical concepts developed were confirmed in experimental studies, the results of which showed that our method could produce, abundantly, black silicon wafers in an environmentally friendly manner compared to traditional chemical etching.
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Barbosa, Hélder M. C., Marta M. D. Ramos, and Helena M. G. Correia. "Computational Study of the Influence of Polymer/Polymer Interface Formation on Bilayer-LED Functioning." Materials Science Forum 636-637 (January 2010): 325–31. http://dx.doi.org/10.4028/www.scientific.net/msf.636-637.325.
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The actual interest on polymer light emitting diodes (PLEDs) is based on the fact that they are easy to process, which reduces the cost of fabrication and thus opening a new branch in the electronic market – the low-cost electronics. However, these devices present a limited efficiency compared to their inorganic counterparts mainly due to the unbalanced charge injection, which reduces the fluorescence emission. One of the first strategies to improve PLEDs efficiency was using a bilayer structure composed by two polymers to improve charge injection and transport, and at the same time tune charge recombination zone to reduce the effect of the electrodes on exciton quenching. Although this is a very ingenious device architecture some of these bilayer devices showed a lower efficiency than it was expected. The reason for that is attributed to the dissolution of the first polymer layer by the solvent used for the deposition of the second polymer layer, which do not allow to create a define polymer/polymer interface. Although cross-linking the first polymer layer can solve this problem, there is not a clear understanding why the presence of a graded interface between both polymer layers can lead to a change on PLED efficiency. In order to clarify the effect of a graded polymer/polymer interface as compared to a sharp one on the functioning of a PLED, we performed computer experiments using a mesoscopic model of a bilayer PLED developed by us that considers the morphology of both polymers at nanoscale and their properties at molecular scale. The results present in this work show clearly a significant change on the charge recombination profile within the polymer device depending on the type of interface formed between the two polymers, which can be a plausible explanation for the loss of efficiency in the bilayer 7-CN-PPV/PPV LED.
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Verga, F. M., G. Giglio, F. Masserano, and L. Ruvo. "Validation of Near-Wellbore Fracture-Network Models With MDT." SPE Reservoir Evaluation & Engineering 5, no. 02 (April 1, 2002): 116–25. http://dx.doi.org/10.2118/77298-pa.
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Summary A new approach was attempted to validate the reconstructed internal geometry of a fractured reservoir by reproducing the reservoir dynamic behavior monitored during modular dynamic tests (MDTs). The description of the reservoir fracture network was achieved by integrating relevant data that could be collected from wireline logs, conventional cores, small drilling-mud-loss analysis, and field-scale observations from outcrop analog inspection. Fracture types, properties, and distributions were thus defined, and a static model of the fractured reservoir was generated stochastically. The dynamic behavior of the fractured system was reproduced by a finite-element flow model. Consistency was required between the observed and simulated pressure data to ensure that the reservoir geometry was modeled adequately. Analysis of the model response as a function of the assigned fracture parameters and comparison between the observed and simulated dynamic behavior allowed achievement of a satisfactory description of the reservoir effective fracture network. Introduction This paper presents the procedure applied to generate and validate the model of near-wellbore regions for an oil-bearing fractured reservoir. The described procedure is considered a strategic part of a newly elaborated methodology aimed at better characterizing classical dual-porosity systems.1 In fact, there is a common feeling that improved description and understanding of fractured reservoirs is needed, as is apparent by analogous integrated procedures recently suggested or outlined by other authors.2-6 The developed methodology is mainly based on the definition of a certain number of structural segments and/or near-wellbore regions inside the reservoir. Fracture distributions are generated stochastically within each region, according to all the available data, to reproduce the rock-fracture network. The dynamic behavior of the fracture-network model is then simulated and compared to the observed production-test responses until a satisfactory match is achieved by the appropriate tuning of the model parameters. Once the dynamic model has been calibrated, the equivalent fracture and matrix parameters (i.e., fracture porosity, fracture permeability, matrix block size, and sigma factor) are obtained and extrapolated to the whole reservoir by adoption of appropriate drivers (such as lithology, stress field, and curvature), and they are selected according to their respective significance for the reservoir under study.3,5 In particular, the case study discussed in this paper is focused on the generation and calibration of a fracture-network model that reproduces the reservoir region surrounding the well at which all the data have been collected. The fracture pattern and aperture were statistically defined by the integration of data obtained from image-log recordings, conventional core analyses, drilling-mud-loss interpretations, and observations on outcrop analogs. Only the properties of the main fractures intercepted by the wellbore were deterministically assigned to the model. Image logs and cores from another nearby well were also considered to verify the consistency on the fracture pattern characterization. Upscaling of the fracture distributions observed at the wellbore and at core scale was required to generate a representative model of the formation. A finite-element model of the fracture network was then generated to properly describe the fluid flow in the reservoir, whereas the flow in the matrix was simulated according to a generic matrix-block approach.6,7 Simulations of the model dynamic behavior were performed to reproduce the pressure response recorded during the MDTs. Comparison between simulation results and measured pressure data allowed verification of the model consistency and calibration of the fracture intensity and permeability.3,6 Field Information The investigated reservoir is an oil-bearing, fractured formation mainly made up of massive, unstratified, tight calcareous dolomite (carbonate platform). The field is an elongated, strongly faulted, northwest/southeast-trending anticline located above a northeast-verging thrust zone, which gently dips toward the southwest. The gross reservoir thickness at the well is approximately 400 m. The oil is strongly undersaturated at the initial reservoir conditions, and the oil density is 32°API. According to the 3D seismic interpretation, two dominant fault sets can be observed. The main set is oriented northwest/southeast, whereas the orientation of the second set is slightly different (north-northwest/south-southeast). A minor set, oriented northeast/ southwest and constituted by small faults rarely exceeding 1 km in length, is also present. The reservoir formations crop out approximately 10 to 15 km south of the field: several structural studies, carried out both at macroscopic scale (geological maps and aerial photographs) and at mesoscopic scale (outcrop), are available for this analogue. According to the geological maps, two fault sets are present, oriented northwest/southeast and northeast/southwest, respectively; the former is more intense and shows a little dispersion in the strike distribution. Aerial photos show the existence of some north-northeast/ south-southwest-trending lineations, younger than the previously described faults. The length of these lineations ranges between 0.5 and 1 km. Outcrop data show three main fracture sets (oriented north-northeast/south-southwest, west-northwest/east-southeast, and northeast/southwest, respectively) more ancient than the outcropping faults. Based on these data, the tectonic history of the area has been subdivided into three main phases:A tensile phase - the carbonate platform was dismembered, and the previously mentioned north-northeast/south-southwest, west-northwest/east-southeast, and northeast/southwest fracture sets were generated.A transpressive phase - the northwest/southeast and northeast/ southwest faults set were created; significant thrusting and backthrusting movements also occurred.A new tensile phase - it is still active and contributes to the reactivation of the old fracture sets (northwest/southeast, northeast/ southwest, and north-northeast/south-southwest-oriented) and to the generation of the regional scale north-northeast/south-southwest- oriented lineations. The status of the present-day stress field also has been studied; the breakout analysis on vertical and deviated wells shows that smin is southwest/northeast-oriented (i.e., it is perpendicular to the direction of the main fracture sets), while smax acts along the vertical direction.
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Shi Zhi-Qi, He Xiao, Liu Lin, and Chen De-Hua. "Wavefield simulation and analysis with finite difference method in partially saturated double-porosity media." Acta Physica Sinica, 2024, 0. http://dx.doi.org/10.7498/aps.73.20240227.
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Double-porosity poroelastic models, which account for the effect of mesoscopic flow in heterogeneous rocks on wave dispersion and attenuation, are useful for quantitative seismic interpretation. Wavefield simulation based on double-porosity models not only helps visualize the propagation characteristics of the elastic waves but also lays the foundation for seismic imaging. In this paper, we perform wavefield simulation and analysis based on the Santos-Rayleigh model which incorporates mesoscopic and global flow in partially-saturated double-porosity media. Specifically, the mesoscopic flow mechanism is represented with a Zener viscoelastic model. The comparison shows that the Zener model can accurately capture the propagation characteristics of fast P-wave, but fails to represent the attenuation characteristics of slow P3 wave in the low-frequency band. It suggests that Zener viscoelastic model and slow wave modes follow different mechanisms. Then staggered grid finite-difference method is used to simulate wave propagation in double-porosity media, and the stiff problem is solved with a time-splitting algorithm, which can significantly improve computational efficiency. Based on above methods, the correctness of our algorithm is verified with derived analytical solution for a P-wave source in a uniform partially saturated poroelastic media. Analytical and numerical solutions are in good agreement and mean error is 0.33%. We provide some examples of wavefield snapshots and seismograms in homogeneous and layered heterogeneous media at seismic and ultrasonic frequencies. Simulation results demonstrate the strong attenuation of fast P-wave and no change of S-wave in the seismic band due to mesoscopic flow mechanism, which is consistent with the theoretical predictions of double-porosity model. Moreover, energy of fast P-wave is concentrated in solid phase while slow waves are stronger in fluid phases. This work contributes to the understanding of broadband elastic wave propagation in heterogeneous partially saturated porous media and can be applied in the reservoir imaging with broadband geophysical data.
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HATZOGLOU, Constantinos, Benjamin Klaes, Fabien Delaroche, Gérald Da Costa, Brian Geiser, Markus Kühbach, Peter B. Wells, and François Vurpillot. "A mesoscopic modelling of field evaporation on atom probe tomography." Journal of Physics D: Applied Physics, May 17, 2023. http://dx.doi.org/10.1088/1361-6463/acd649.
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Abstract Reconstructions in Atom Probe Tomography (APT) are biased by image distortions arising from dynamic changes of the specimen geometry that controls image projection. Despite the strong efforts to build realistic models for understanding and reproducing image artefacts, current models are too slow or not adapted to be routinely used in image correction approaches. To understand the APT imaging process for real size samples submitted to realistic experimental conditions of electric field and temperature, we propose an alternative simulation tool based on a coarse-grained model of the sample surface. The surface electric field on a meshed surface is calculated by using continuous models describing field evaporation. The dynamic evolution of the sample surface and the image projection are predicted using materials properties. We show that the interplay between temperature and electric field is an important ingredient in predicting the ion projection, in pure metals and in more complex materials. This fast approach accurately reproduces the well-known local magnification and trajectory overlaps effects in the evaporation of small particles. By combining prior knowledge about the sample structure and properties, the model could be used to improve the reconstruction approaches for complex sample geometries.
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Corbin, Gregor, Axel Klar, Christina Surulescu, Christian Engwer, Michael Wenske, Juanjo Nieto, and Juan Soler. "Modeling glioma invasion with anisotropy- and hypoxia-triggered motility enhancement: From subcellular dynamics to macroscopic PDEs with multiple taxis." Mathematical Models and Methods in Applied Sciences, December 28, 2020, 1–46. http://dx.doi.org/10.1142/s0218202521500056.
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We deduce a model for glioma invasion that accounts for the dynamics of brain tissue being actively degraded by tumor cells via excessive acidity production, but also according to the local orientation of tissue fibers. Our approach has a multiscale character: we start with a microscopic description of single cell dynamics including biochemical and/or biophysical effects of the tumor microenvironment, translated on the one hand into cell stress and corresponding forces and on the other hand into receptor binding dynamics. These lead on the mesoscopic level to kinetic equations involving transport terms with respect to all considered kinetic variables and eventually, by appropriate upscaling, to a macroscopic reaction–diffusion equation for glioma density with multiple taxis, coupled to (integro-)differential equations characterizing the evolution of acidity and macro- and mesoscopic tissue. Our approach also allows for a switch between fast and slower moving regimes, according to the local tissue anisotropy. We perform numerical simulations to assess the importance of each tactic term and investigate the influence of two models for tissue dynamics on the tumor shape. We also suggest how the model can be used to perform a numerical necrosis-based tumor grading or support radiotherapy planning by dose painting. Finally, we discuss alternative ways of including cell level environmental influences in such a multiscale modeling approach, ultimately leading in the macroscopic limit to (multiple) taxis.
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Venkadesh, Siva, Asmir Shaikh, Heman Shakeri, Ernest Barreto, and John Darrell Van Horn. "Biophysical modulation and robustness of itinerant complexity in neuronal networks." Frontiers in Network Physiology 4 (March 7, 2024). http://dx.doi.org/10.3389/fnetp.2024.1302499.
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Transient synchronization of bursting activity in neuronal networks, which occurs in patterns of metastable itinerant phase relationships between neurons, is a notable feature of network dynamics observed in vivo. However, the mechanisms that contribute to this dynamical complexity in neuronal circuits are not well understood. Local circuits in cortical regions consist of populations of neurons with diverse intrinsic oscillatory features. In this study, we numerically show that the phenomenon of transient synchronization, also referred to as metastability, can emerge in an inhibitory neuronal population when the neurons’ intrinsic fast-spiking dynamics are appropriately modulated by slower inputs from an excitatory neuronal population. Using a compact model of a mesoscopic-scale network consisting of excitatory pyramidal and inhibitory fast-spiking neurons, our work demonstrates a relationship between the frequency of pyramidal population oscillations and the features of emergent metastability in the inhibitory population. In addition, we introduce a method to characterize collective transitions in metastable networks. Finally, we discuss potential applications of this study in mechanistically understanding cortical network dynamics.
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Wagner, Manfred H., Esmaeil Narimissa, and Yuichi Masubuchi. "Elongational viscosity of poly(propylene carbonate) melts: tube-based modelling and primitive chain network simulations." Rheologica Acta, November 12, 2022. http://dx.doi.org/10.1007/s00397-022-01373-w.
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Abstract In fast elongational flows, linear polymer melts exhibit a monotonic decrease of the viscosity with increasing strain rate, even beyond the contraction rate of the polymer defined by the Rouse time. We consider two possible explanations of this phenomenon: (a) the reduction of monomeric friction and (b) the reduction of the tube diameter with increasing deformation leading to an Enhanced Relaxation of Stretch (ERS) on smaller length scales. (Masubuchi et al. (2022) reported Primitive Chain Network (PCN) simulations using an empirical friction reduction model depending on segmental orientation and could reproduce the elongational viscosity data of three poly(propylene carbonate) melts and a polystyrene melt. Here, we show that the mesoscopic tube-based ESR model (Wagner and Narimissa 2021) provides quantitative agreement with the same data set based exclusively on the linear-viscoelastic characterization and the Rouse time. From the ERS model, a parameter-free universal relation of monomeric friction reduction as a function of segmental stretch can be derived. PCN simulations using this friction reduction relation are shown to reproduce quantitatively the experimental data even without any fitting parameter. The comparison with results of the earlier PCN simulation results with friction depending on segmental orientation demonstrates that the two friction relations examined work equally well which implies that the physical mechanisms of friction reduction are still open for discussion.
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Rohwerder, M., E. Hornung, and Xing-Wen Yu. "Delamination of Poylmer Coatings from Metal Substrates: Submicroscopic and Molecular Aspects." MRS Proceedings 734 (2002). http://dx.doi.org/10.1557/proc-734-b2.8.
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Delamination of organic coatings from metal surfaces can occur in a number of different ways, e.g. as pure cathodic delamination, as Filiform corrosion or a mixture of these. In fact, in most technical systems the pure cases are the exception and, of course, delamination is usually very slow. It has been shown that in fast delaminating systems the length scales may range between several 100 μm and several millimetres, while in systems which show slow delamination the reaction zones can be confined to submicroscopic distances [1]. This underlines the importance of investigation methods with submicroscopic resolution. As a very promising new technique Scanning Kelvin Probe Force Microscopy (SKPFM) was applied for the investigation of cathodic delamination and filiform corrosion on a submicroscopic scale [1, 2]. Indeed, these first investigations have shown that SKPFM gives basically the same information as the standard Scanning Kelvin Probe (SKP), but with a much improved resolution. It could be shown, for instance, that the extension of the reaction zone seems to be much narrower than would have to be assumed from the SKP measurements. Based on the knowledge about the different delamination types that was obtained from investigations with the standard SKP [3–12] the SKPFM should be the ideal tool to get information on the submicroscopic scale. However, SKPFM alone is not sufficient for revealing the underlying fundamental mechanisms; of even higher importance is the knowledge of the molecular and mesoscopic structure at the buried interface. In this paper a design for suitable model samples is proposed and first results are presented.
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Francis, Robert J., Gillian Robb, Lee McCann, Bhagwati Khatri, James Keeble, Belinda Dagg, Brad Amos, et al. "Three-dimensional in situ morphometrics of Mycobacterium tuberculosis infection within lesions by optical mesoscopy and novel acid-fast staining." Scientific Reports 10, no. 1 (December 2020). http://dx.doi.org/10.1038/s41598-020-78640-4.
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AbstractTuberculosis (TB) preclinical testing relies on in vivo models including the mouse aerosol challenge model. The only method of determining colony morphometrics of TB infection in a tissue in situ is two-dimensional (2D) histopathology. 2D measurements consider heterogeneity within a single observable section but not above and below, which could contain critical information. Here we describe a novel approach, using optical clearing and a novel staining procedure with confocal microscopy and mesoscopy, for three-dimensional (3D) measurement of TB infection within lesions at sub-cellular resolution over a large field of view. We show TB morphometrics can be determined within lesion pathology, and differences in infection with different strains of Mycobacterium tuberculosis. Mesoscopy combined with the novel CUBIC Acid-Fast (CAF) staining procedure enables a quantitative approach to measure TB infection and allows 3D analysis of infection, providing a framework which could be used in the analysis of TB infection in situ.
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Wang, Enjiang, Lin Zhang, José M. Carcione, and Jing Ba. "Effect of mesoscopic-flow loss on seismic reflections in media with penny-shaped inclusions." Geophysical Journal International, July 8, 2022. http://dx.doi.org/10.1093/gji/ggac261.
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Summary We obtain the amplitude and energy reflection coefficients of seismic waves in porous media with penny-shaped inclusions, based on the generalized Biot-Rayleigh model that takes into account the attenuation due to mesoscopic local fluid flow (LFF). We consider two cases, including a contact between two porous media having either different fluids (gas-water contact) or crack density/aspect ratio, as well as a water half-space overlying a porous medium, and study the frequency-dependent reflection-transmission (scattering) coefficients for open- and sealed-pore boundary conditions. Our examples show that the LFF mechanism mainly reduces the reflection coefficients (amplitude and energy) at the gas-water contact and at a water/porous-medium interface for frequencies less than 10 kHz, due to the fact that the velocity in the lower medium decreases. For the latter case, if the fluid is gas, the LFF effect becomes only important at frequencies between 0.0001 and 10 Hz for the open-pore case. This is due to the fact that the acoustic impedance contrast between water and gas is high. At frequencies less than 0.0001 Hz, the interface is equivalent to a water/elastic-medium one, and hence the results are the same as those of the sealed-pore case. Moreover, the crack density and aspect ratio affect the mesoscopic attenuation and relaxation frequency, and therefore the reflection coefficients.
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Chung, Brandon, Adam Schwartz, Bartley Ebbinghaus, Michael Fluss, Jeffrey Haslam, Kerri Blobaum, and James Tobin. "Spectroscopic Signature of Aging in δ-Pu(Ga)." MRS Proceedings 893 (2005). http://dx.doi.org/10.1557/proc-0893-jj03-04.
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AbstractPlutonium, because of its radioactive nature, ages from the “inside out” by means of self-irradiation damage and thus produces nanoscale internal defects. The self-irradiation induced defects come in the form of Frenkel-type defects (vacancies and self-interstitial atoms), helium in-growth, and defect clusters. At present there are neither experimental nor theoretical models describing the changes in the electronic structure caused by the aging in Pu. This fact appears to be associated primarily with the absence of reasonably convincing spectroscopic evidence of the changes. This paper demonstrates that Resonant Photoemission, a variant of Photoelectron Spectroscopy, has strong sensitivity to aging of Pu samples. The spectroscopic results are correlated with an extra-atomic screening model, and are shown to be the fingerprint of mesoscopic or nanoscale internal damage in the Pu physical structure. This means that a spectroscopic signature of internal damage due to aging in Pu has been established.
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Abdul-Latif, A., and M. Chadli. "Determinist-Probabilistic Concept in Modeling Fatigue Damage Through a Micromechanical Approach." Journal of Engineering Materials and Technology 132, no. 1 (November 2, 2009). http://dx.doi.org/10.1115/1.3184029.
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Motivated by a micromechanical determinist-probabilistic model coupled with damage recently developed by the authors, a new generalization is proposed to describe the nonlinear elasto-inelastic cyclic strain-stress behavior of polycrystals notably under biaxial cyclic loading paths. In this context, this generalization considers a compressible and linear anisotropic granular elastic strain behavior coupled with damage. The model is expressed in the framework of the time dependent plasticity for a small strain assumption. It is assumed that a damage variable initiates at the mesoscopic (granular) level where the plastic strain localization phenomenon takes place. The associated thermodynamic force of the damage variable is determined using the concept of total granular energy (elastic and inelastic). The transition of the elastic strain from the single to the polycrystal is modified due to its explicit coupling with damage. Comparisons between predicted and experimental results are conducted describing the low-cycle fatigue behavior of the aluminum alloy 2024 under different complex cyclic loading paths. It is demonstrated that the model has a reasonable ability in describing the cyclic behavior of this alloy. Qualitatively, the model is tested under different cyclic loading paths with stress-controlled condition describing especially the ratcheting behavior of the alloy. In fact, the effects of the applied mean stress on the predicted overall elasto-inelastic behavior and on the fatigue life are carefully studied. It shows the dependence of the fatigue life on the mean stress value.
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Bai Jian-Nan, Han Song, Chen Jian-Di, Han Hai-Yan, and Yan Dong. "Correlated collective excitation and quantum entanglement between two Rydberg superatoms in the steady state." Acta Physica Sinica, 2023, 0. http://dx.doi.org/10.7498/aps.72.20222030.
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Owing to the unique physical characteristics of Rydberg atoms, which play an important role in quantum information and quantum computation, the theoretical and applied research of Rydberg atoms have become one of the hot spots of scientific research in recent years. Thanks to the large polarizability of Rydberg atoms, even a small electric field could cause a considerable electric dipole moment, resulting in a strong dipole-dipole interaction between Rydberg atoms. The multiple excitations of the Rydberg states are strongly inhibited because of the strong dipole interaction between atoms within a mesoscopic interaction (blockade) region. We call this phenomenon the dipole blockade effect. The dipole blockade regime allows us to build single-photon quantum devices, implement quantum gates, generate quantum entanglement, simulate many-body quantum problems and so on.<br/>A Rydberg atomic ensemble in the same blockade region can be regarded as a superatom. In the same way, if these atoms trapped in two optical dipole traps, each sub-ensemble can be considered as a sub-superatom which is closely related to the superatom. Based on the fact that two Rydberg sub-superatoms will be strongly correlated due to sharing no more than one excited Rydberg atom, we study the correlated collective excitation and the quantum entanglement between two Rydberg sub-superatoms in the steady state. With the superatom model, the problem of exponentially increasing system size with the number of atoms can be circumvented to a certain extent in studying many-body physics. By solving the two body Lindblad's master equation accurately, we obtain the analytical expressions for the collective excitation probabilities of the two sub-superatoms, and the concurrence measuring the bipartite entanglement between them. Our results show that they are all sensitive to the number of each Rydberg superatom:the bigger (including more atoms) the Rydberg superatom, the higher the collective Rydberg excitation probability; the maximally entangled state can only be obtained with two equal-sized Rydberg superatoms. When this condition is fulfilled, the generation of mesoscopic entanglement could be achieved by adding the number of each Rydberg superatom. This may provide an attractive platform to study the quantum-classical correspondence and have potential promising applications in quantum information processing.
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Ogurtani, Tarik Omer. "Mesoscopic irreversible thermodynamics of aging kinetics of alpha polypeptides [DNA] under various constraints: Special reference to the simple spring mechanics." AIP Advances 14, no. 2 (February 1, 2024). http://dx.doi.org/10.1063/5.0183144.
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The mesoscopic irreversible thermodynamic treatment of α-polypeptides and the helical polynucleotides (DNA) furnishes two sets of analytical expressions, which allow us not only to analyze the reversible force–extension experiments performed by atomic force microscopy (AFM) but also to predict the irreversible “aging” kinetics of the single-stranded and double-stranded polynucleotides (ssDNA and dsDNA) helical conformations exposed to aqueous solutions and applied static stress systems under the various constraints. The present physicochemical cage model emphasizes the fact that the global Helmholtz free energy of the helical conformation acts not only under the stored “intrinsic” unusual torsional and bending elastic energies inherited by the unfolded helical structure of the amino-acid (peptides) or the nucleic-acid (nucleotide) backbone but also reveals the importance of the interfacial Helmholtz free energy density associated with the interaction of the side-wall branches within the surrounding aqueous solutions. The analytical expression obtained for the unfolding force vs extension (FE) shows a strong non-linear elasticity behavior under the twist angle constraint when the interfacial Helmholtz energy term is incorporating into the scenario. This behavior is in excellent quantitative agreement with the AFM test results obtained by Idiris et al. (2000) on the poly-L-glutamic acid [Glu(n)-Cys] exposed to aqueous solutions, which show that acidity increases the degrees of helicity.
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Ovečka, Miroslav, Jiří Sojka, Michaela Tichá, George Komis, Jasim Basheer, Cintia Marchetti, Olga Šamajová, Lenka Kuběnová, and Jozef Šamaj. "Imaging plant cells and organs with light-sheet and super-resolution microscopy." Plant Physiology, August 26, 2021. http://dx.doi.org/10.1093/plphys/kiab349.
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Abstract The documentation of plant growth and development requires integrative and scalable approaches to investigate and spatiotemporally resolve various dynamic processes at different levels of plant body organization. The present update deals with vigorous developments in mesoscopy, microscopy and nanoscopy methods that have been translated to imaging of plant subcellular compartments, cells, tissues and organs over the past 3 years with the aim to report recent applications and reasonable expectations from current light-sheet fluorescence microscopy (LSFM) and super-resolution microscopy (SRM) modalities. Moreover, the shortcomings and limitations of existing LSFM and SRM are discussed, particularly for their ability to accommodate plant samples and regarding their documentation potential considering spherical aberrations or temporal restrictions prohibiting the dynamic recording of fast cellular processes at the three dimensions. For a more comprehensive description, advances in living or fixed sample preparation methods are also included, supported by an overview of developments in labeling strategies successfully applied in plants. These strategies are practically documented by current applications employing model plant Arabidopsis thaliana (L.) Heynh., but also robust crop species such as Medicago sativa L. and Hordeum vulgare L. Over the past few years, the trend towards designing of integrative microscopic modalities has become apparent and it is expected that in the near future LSFM and SRM will be bridged to achieve broader multiscale plant imaging with a single platform.