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clotFoam: An Open-Source Framework to Simulate Blood Clot Formation Under Arterial Flow

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arXiv 2023年

作者： Montgomery, David Municchi, Federico Leiderman, Karin Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Department of Mechanical Engineering Colorado School of Mines 1500 Illinois St GoldenCO80401 United States Department of Mathematics University of North Carolina at Chapel Hill 216 Lenoir Dr Chapel HillNC27599 United States Computational Medicine Program University of North Carolina at Chapel Hill 216 Lenoir Dr Chapel HillNC27599 United States

Blood clotting involves the coupled processes of platelet aggregation and coagulation. Simulating clotting under flow in complex geometries is challenging due to multiple temporal and spatial scales and high computational cost. clotFoam is an open-source software developed in OpenFOAM that employs a continuum model of platelet advection, diffusion, and aggregation in a dynamic fluid environment and a simplified coagulation model with proteins that advect, diffuse, and react within the fluid and with wall-bound species through reactive boundary conditions. Our framework provides the foundation on which one can build more complex models and perform reliable simulations in almost any computational domain. © 2023, CC BY.

关键词： Coagulation

Flagellum Pumping Efficiency in Shear-Thinning Viscoelastic Fluids

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arXiv 2023年

作者： Barrett, Aaron Fogelson, Aaron L. Gregory Forest, M. Gruninger, Cole Lim, Sookkyung Griffith, Boyce E. Department of Mathematics University of Utah Salt Lake CityUT United States Departments of Mathematics and Biomedical Engineering University of Utah Salt Lake CityUT United States Department of Mathematics University of North Carolina Chapel HillNC United States Department of Applied Physical Sciences University of North Carolina Chapel HillNC United States Department of Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Department of Mathematical Sciences University of Cincinnati CincinnatiOH United States Computational Medicine Program University of North Carolina School of Medicine Chapel HillNC United States McAllister Heart Institute University of North Carolina School of Medicine Chapel HillNC United States

Microorganism motility often takes place within complex, viscoelastic fluid environments, e.g., sperm in cervicovaginal mucus and bacteria in biofilms. In such complex fluids, strains and stresses generated by the microorganism are stored and relax across a spectrum of length and time scales and the complex fluid can be driven out of its linear response regime. Phenomena not possible in viscous media thereby arise from feedback between the swimmer and the complex fluid, making swimming efficiency co-dependent on the propulsion mechanism and fluid properties. Here we parameterize a flagellar motor and filament properties together with elastic relaxation and nonlinear shear-thinning properties of the fluid in a computational immersed boundary model. We then explore swimming efficiency, defined as a particular flow rate divided by the torque required to spin the motor, over this parameter space. Our findings indicate that motor efficiency (measured by the volumetric flow rate) can be boosted or degraded by relatively moderate or strong shear-thinning of the viscoelastic environment. Copyright © 2023, The Authors. All rights reserved.

关键词： Shear thinning

Ab initio quantum many-body description of superconducting trends in the cuprates

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arXiv 2023年

作者： Cui, Zhi-Hao Yang, Junjie Tölle, Johannes Ye, Hong-Zhou Yuan, Shunyue Zhai, Huanchen Park, Gunhee Kim, Raehyun Zhang, Xing Lin, Lin Berkelbach, Timothy C. Chan, Garnet Kin-Lic Division of Chemistry and Chemical Engineering California Institute of Technology PasadenaCA91125 United States Department of Chemistry Columbia University New YorkNY10027 United States Division of Engineering and Applied Science California Institute of Technology PasadenaCA91125 United States Department of Mathematics University of California BerkeleyCA94720 United States Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

Using a systematic ab initio quantum many-body approach that goes beyond low-energy models, we directly compute the superconducting pairing order and estimate the pairing gap of several doped cuprate materials and structures within a purely electronic picture. We find that we can correctly capture two well-known trends: the pressure effect, where the pairing order and gap increase with intra-layer pressure, and the layer effect, where the pairing order and gap vary with the number of copper-oxygen layers. From these calculations, we observe that the strength of superexchange and the covalency at optimal doping are the best descriptors for these trends. Our microscopic analysis further identifies that strong short-range spin fluctuations and multi-orbital charge fluctuations drive the development of the pairing order. Our work illustrates the possibility of a material-specific ab initio understanding of unconventional high-temperature superconducting materials. Copyright © 2023, The Authors. All rights reserved.

关键词： High temperature superconductors

Benchmarking the Immersed Boundary Method for Viscoelastic Flows

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arXiv 2023年

作者： Gruninger, Cole Barrett, Aaron Fang, Fuhui Forest, M. Gregory Griffith, Boyce E. Department of Mathematics University North Carolina Chapel HillNC United States Department of Mathematics University of Utah Salt Lake CityUT United States Department of Applied Physical Sciences University of North Carolina Chapel HillNC United States Department of Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina School of Medicine Chapel HillNC United States McAllister Heart Institute University of North Carolina School of Medicine Chapel HillNC United States

We present and analyze a series of benchmark tests regarding the application of the immersed boundary (IB) method to viscoelastic flows through and around non-trivial, stationary geometries. The IB method is widely used for the simulation of biological fluid dynamics and other modeling scenarios where a structure is immersed in a fluid. Although the IB method has been most commonly used to model systems with viscous incompressible fluids, it also can be applied to visoelastic fluids, and has enabled the study of a wide variety of dynamical problems including the settling of vesicles and the swimming of elastic filaments in fluids modeled by the Oldroyd-B constuitive equation. However, to date, relatively little work has explored the accuracy or convergence properties of the numerical scheme. Herein, we present benchmarking results for an IB solver applied to viscoelastic flows in and around non-trivial geometries using the idealized Oldroyd-B and more realistic, polymer-entanglement-based Rolie-Poly constitutive equations. We use two-dimensional numerical test cases along with results from rheology experiments to benchmark the IB method and compare it to more complex finite element and finite volume viscoelastic flow solvers. Additionally, we analyze different choices of regularized delta function and relative Lagrangian grid spacings which allow us to identify and recommend the key choices of these numerical parameters depending on the present flow regime. Copyright © 2023, The Authors. All rights reserved.

关键词： Benchmarking

Subdiffusive wave transport and weak localization transition in three-dimensional stealthy hyperuniform disordered systems

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Physical Review B 2022年第6期105卷 064204-064204页

作者： F. Sgrignuoli S. Torquato L. Dal Negro Department of Electrical and Computer Engineering & Photonics Center Boston University 8 Saint Mary's Street Boston Massachusetts 02215 USA Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08540 USA Division of Material Science and Engineering Boston University 15 Saint Mary's Street Brookline Massachusetts 02446 USA Department of Physics Boston University 590 Commonwealth Avenue Boston Massachusetts 02215 USA

The purpose of this work is to understand the fundamental connection between structural correlations and light localization in three-dimensional (3D) open scattering systems of finite size. We numerically investigate the transport of vector electromagnetic waves scattered by resonant electric dipoles spatially arranged in 3D space by stealthy hyperuniform disordered point patterns. Three-dimensional stealthy hyperuniform disordered systems are engineered with different structural correlation properties determined by their degree of stealthiness χ. Such fine control of exotic states of amorphous matter enables the systematic design of optical media that interpolate in a tunable fashion between uncorrelated random structures and crystalline materials. By solving the electromagnetic multiple scattering problem using Green's matrix spectral method, we establish a transport phase diagram that demonstrates a distinctive transition from a diffusive to a weak localization regime beyond a critical scattering density that depends on χ. The transition is characterized by studying the Thouless number and the spectral statistics of the scattering resonances. In particular, by tuning the χ parameter, we demonstrate large spectral gaps and suppressed subradiant proximity resonances, facilitating light localization. Moreover, consistently with previous studies, our results show a region of the transport phase diagram where the investigated scattering systems become transparent. Our work provides a systematic description of the transport and weak localization properties of light in stealthy hyperuniform structures and motivates the engineering of photonic systems with enhanced light-matter interactions for applications to both classical and quantum devices.

关键词： Anderson localization Light-matter interaction Mesoscopics Photonics Scattering theory Weak localization Metamaterials

Cross-system biological image quality enhancement based on the generative adversarial network as a foundation for establishing a multi-institute microscopy cooperative network

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arXiv 2024年

作者： Panek, Dominik Rząca, Carina Szczypior, Maksymilian Sorysz, Joanna Misztal, Krzysztof Baster, Zbigniew Rajfur, Zenon Doctoral School of Exact and Natural Sciences Jagiellonian University ul. Lojasiewicza 11 Kraków30-348 Poland Department of Molecular and Interfacial Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate Program in Biophysics Faculty of Physics Astronomy and Applied Computer Science Jagiellonian University ul. Lojasiewicza 11 Kraków30‑348 Poland Undergraduate program in Biomedical Engineering Faculty of Electrical Engineering Automatics Computer Science and Biomedical Engineering AGH University of Science and Technology Al. A. Mickiewicza 30 Building B-1 Kraków30-059 Poland Division of Computational Mathematics Faculty of Mathematics and Computer Science Jagiellonian University 6 Lojasiewicza St. Kraków Poland

High-quality fluorescence imaging of biological systems is limited by processes like photobleaching and phototoxicity, and also in many cases, by limited access to the latest generations of microscopes. Moreover, low temporal resolution can lead to a motion blur effect in living systems. Our work presents a deep learning (DL) generative-adversarial approach to the problem of obtaining high-quality (HQ) images based on their low-quality (LQ) equivalents. We propose a generative-adversarial network (GAN) for contrast transfer between two different separate microscopy systems: a confocal microscope (producing HQ images) and a wide-field fluorescence microscope (producing LQ images). Our model proves that such transfer is possible, allowing us to receive HQ-generated images characterized by low mean squared error (MSE) values, high structural similarity index (SSIM), and high peak signal-to-noise ratio (PSNR) values. For our best model in the case of comparing HQ-generated images and HQ-ground truth images, the median values of the metrics are 6·10-4, 0.9413, and 31.87, for MSE, SSIM, and PSNR, respectively. In contrast, in the case of comparison between LQ and HQ ground truth median values of the metrics are equal to 0.0071, 0.8304, and 21.48 for MSE, SSIM, and PSNR respectively. Therefore, we observe a significant increase ranging from 14% to 49% for SSIM and PSNR respectively. These results, together with other single-system cross-modality studies, provide proof of concept for further implementation of a cross-system biological image quality enhancement. © 2024, CC BY-SA.

关键词： Fluorescence imaging

Interacting models for twisted bilayer graphene: a quantum chemistry approach

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arXiv 2022年

作者： Faulstich, Fabian M. Stubbs, Kevin D. Zhu, Qinyi Soejima, Tomohiro Dilip, Rohit Zhai, Huanchen Kim, Raehyun Zaletel, Michael P. Chan, Garnet Kin-Lic Lin, Lin Department of Mathematics University of California BerkeleyCA94720 United States Department of Physics University of California BerkeleyCA94720 United States Division of Chemistry and Chemical Engineering California Institute of Technology PasadenaCA91125 United States Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

The nature of correlated states in twisted bilayer graphene (TBG) at the magic angle has received intense attention in recent years. We present a numerical study of an interacting Bistritzer-MacDonald (IBM) model of TBG using a suite of methods in quantum chemistry, including Hartree-Fock, coupled cluster singles, doubles (CCSD), and perturbative triples (CCSD(T)), as well as a quantum chemistry formulation of the density matrix renormalization group method (DMRG). Our treatment of TBG is agnostic to gauge choices, and hence we present a new gauge-invariant formulation to detect the spontaneous symmetry breaking in interacting models. To benchmark our approach, we focus on a simplified spinless, valleyless IBM model. At integer filling (ν = 0), all numerical methods agree in terms of energy and C2zT symmetry breaking. Additionally, as part of our benchmarking, we explore the impact of different schemes for removing "double-counting" in the IBM model. Our results at integer filling suggest that cross-validation of different IBM models may be needed for future studies of the TBG system. After benchmarking our approach at integer filling, we perform the first systematic study of the IBM model near integer filling (for |ν| Copyright © 2022, The Authors. All rights reserved.

关键词： Quantum chemistry

computational design of anisotropic stealthy hyperuniform composites with engineered directional scattering properties

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Physical Review E 2023年第4期108卷 045306-045306页

作者： Wenlong Shi David Keeney Duyu Chen Yang Jiao Salvatore Torquato Materials Science and Engineering Arizona State University Tempe Arizona 85287 USA Materials Research Laboratory University of California Santa Barbara California 93106 USA Department of Physics Arizona State University Tempe Arizona 85287 USA Department of Chemistry Princeton University Princeton New Jersey 08544 USA Department of Physics Princeton University Princeton New Jersey 08544 USA Princeton Institute of Materials Princeton University Princeton New Jersey 08544 USA Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Disordered hyperuniform materials are an emerging class of exotic amorphous states of matter that endow them with singular physical properties, including large isotropic photonic band gaps, superior resistance to fracture, and nearly optimal electrical and thermal transport properties, to name but a few. Here we generalize the Fourier-space-based numerical construction procedure for designing and generating digital realizations of isotropic disordered hyperuniform two-phase heterogeneous materials (i.e., composites) developed by Chen and Torquato [Acta Mater. 142, 152 (2018)] to anisotropic microstructures with targeted spectral densities. Our generalized construction procedure explicitly incorporates the vector-dependent spectral density function χ̃V(k) of arbitrary form that is realizable. We demonstrate the utility of the procedure by generating a wide spectrum of anisotropic stealthy hyperuniform microstructures with χ̃V(k)=0 for k∈Ω, i.e., complete suppression of scattering in an “exclusion” region Ω around the origin in Fourier space. We show how different exclusion-region shapes with various discrete symmetries, including circular-disk, elliptical-disk, square, rectangular, butterfly-shaped, and lemniscate-shaped regions of varying size, affect the resulting statistically anisotropic microstructures as a function of the phase volume fraction. The latter two cases of Ω lead to directionally hyperuniform composites, which are stealthy hyperuniform only along certain directions and are nonhyperuniform along others. We find that while the circular-disk exclusion regions give rise to isotropic hyperuniform composite microstructures, the directional hyperuniform behaviors imposed by the shape asymmetry (or anisotropy) of certain exclusion regions give rise to distinct anisotropic structures and degree of uniformity in the distribution of the phases on intermediate and large length scales along different directions. Moreover, while the anisotropic exclusion regions

关键词： Amorphous materials Complex materials Simulated annealing

An Immersed Interface Method for Incompressible Flows and Geometries with Sharp Features

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arXiv 2024年

作者： Facci, Michael J. Kolahdouz, Ebrahim M. Griffith, Boyce E. Department of Mathematics University of North Carolina Chapel HillNC United States Flatiron Institute Simons Foundation New YorkNY United States Department of Biomedical Engineering University of North Carolina Chapel HillNC United States Carolina Center for Interdisciplinary Applied Mathematics University of North Carolina Chapel HillNC United States Computational Medicine Program University of North Carolina School of Medicine Chapel HillNC United States McAllister Heart Institute University of North Carolina School of Medicine Chapel HillNC United States

The immersed interface method (IIM) for models of fluid flow and fluid-structure interaction imposes jump conditions that capture stress discontinuities generated by forces that are concentrated along immersed boundaries. Most prior work using the IIM for fluid dynamic applications has focused on smooth interfaces, but boundaries with sharp features such as corners and edges can appear in practical analyses, particularly on engineered structures. The present study builds on our work to integrate finite element-type representations of interface geometries with the IIM. Initial realizations of this approach used a continuous Galerkin (CG) finite element discretization for the boundary, but as we show herein, these approaches generate large errors near sharp geometrical features. To overcome this difficulty, this study introduces an IIM approach using discontinuous Galerkin (DG) representation of the jump conditions. Numerical examples explore the impacts of different interface representations on accuracy for both smooth and sharp boundaries, particularly flows interacting with fixed interface configurations. We demonstrate that using a DG approach provides accuracy that is comparable to the CG method for smooth cases. Further, we identify a time step size restriction for the CG representation that is directly related to the sharpness of the geometry. In contrast, time step size restrictions imposed by DG representations are demonstrated to be insensitive to the presence of sharp *** Codes 76-10 (Primary) 76D05 (Secondary) © 2024, CC BY-NC-ND.

关键词： Incompressible flow