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arXiv 2022年

作者： Partin, Lauren Schiavazzi, Daniele E. Long, Carlos A. Sing Department Of Applied And Computational Mathematics And Statistics University Of Notre Dame Notre DameIN United States Institute For Mathematical And Computational Engineering Institute For Biological And Medical Engineering Pontificia Universidad Católica De Chile Santiago Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For The Discovery Of Structures In Complex Data Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For Cardiovascular Magnetic Resonance Chile

Novel Magnetic Resonance (MR) imaging modalities can quantify hemodynamics but require long acquisition times, precluding its widespread use for early diagnosis of cardiovascular disease. To reduce the acquisition times, reconstruction methods from undersampled measurements are routinely used, that leverage representations designed to increase image compressibility. Reconstructed anatomical and hemodynamic images may present visual artifacts. Although some of these artifact are essentially reconstruction errors, and thus a consequence of undersampling, others may be due to measurement noise or the random choice of the sampled frequencies. Said otherwise, a reconstructed image becomes a random variable, and both its bias and its covariance can lead to visual artifacts;the latter leads to spatial correlations that may be misconstrued for visual information. Although the nature of the former has been studied in the literature, the latter has not received as much attention. In this study, we investigate the theoretical properties of the random perturbations arising from the reconstruction process, and perform a number of numerical experiments on simulated and MR aortic flow. Our results show that the correlation length remains limited to two to three pixels when a Gaussian undersampling pattern is combined with recovery algorithms based on 1-norm minimization. However, the correlation length may increase significantly for other undersampling patterns, higher undersampling factors (i.e., 8× or 16× compression), and different reconstruction methods. © 2022, CC BY-NC-ND.

关键词： Magnetic resonance

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Finite-thickness effect of the fluids on bubbles and spikes in Richtmyer–Meshkov instability for arbitrary Atwood numbers

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Plasma Science and Technology 2019年第2期21卷 9-15页

作者： Wanhai LIU Changping YU Pei WANG Zheng FU Lili WANG Yulian CHEN Research Center of Computational Physics Mianyang Normal University LHD Institute of MechanicsChinese Academy of Sciences Institute of Applied Physics and Computational Mathematics Mechanical and Electrical Engineering Department Lanzhou Resources and Environment Voc-Tech College

This paper investigates the finite-thickness effect of two superimposed fluids on bubbles and spikes in Richtmyer–Meshkov instability(RMI) for arbitrary Atwood numbers by using the method of the small parameter expansion up to the second order. When the thickness of the two fluids tends to be infinity, our results can reproduce the classical results where RMI happens at the interface separating two semi-infinity-thickness fluids of different densities. It is found that the thickness has a large influence on the amplitude evolution of bubbles and spikes compared with those in classical RMI. Based on the thickness relationship of the two fluids, the thickness effect on bubbles and spikes for four cases is discussed. The thickness encourages(or reduces)the growth of bubbles or spikes, depending on not only Atwood number, but also the relationship of the thickness ratio of the heavy and light fluids, which is explicitly determined in this paper.

关键词： Richtmyer–Meshkov instability bubbles and spikes finite-thickness

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Foundation Models for Atomistic Simulation of Chemistry and Materials

arXiv

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arXiv 2025年

作者： Yuan, Eric C.-Y. Liu, Yunsheng Chen, Junmin Zhong, Peichen Raja, Sanjeev Kreiman, Tobias Vargas, Santiago Xu, Wenbin Head-Gordon, Martin Yang, Chao Blau, Samuel M. Cheng, Bingqing Krishnapriyan, Aditi Head-Gordon, Teresa Kenneth S. Pitzer Theory Center Department of Chemistry United States Department of Chemical and Biomolecular Engineering United States Electrical Engineering and Computer Science United States Bakar Institute of Digital Materials for the Planet University of California BerkeleyCA94720 United States Chemical Sciences Division United States Applied Mathematics and Computational Research Division United States Energy Technologies Area United States National Energy Research Scientific Computing Center Lawrence Berkeley National Laboratory BerkeleyCA94720 United States

Given the power of large language and large vision models, it is of profound and fundamental interest to ask if a foundational model based on data and parameter scaling laws and pre-training strategies is possible for learned simulations of chemistry and materials. The scaling of large and diverse datasets and highly expressive architectures for chemical and materials sciences should result in a foundation model that is more efficient and broadly transferable, robust to out-of-distribution challenges, and easily fine-tuned to a variety of downstream observables, when compared to specific training from scratch on targeted applications in atomistic simulation. In this Perspective we aim to cover the rapidly advancing field of machine learned interatomic potentials (MLIP), and to illustrate a path to create chemistry and materials MLIP foundation models at larger scale. © 2025, CC BY-SA.

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Machine-learning-based non-Newtonian fluid model with molecular fidelity

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Physical Review E 2020年第4期102卷 043309-043309页

作者： Huan Lei Lei Wu Weinan E Department of Computational Mathematics Science & Engineering and Department of Statistics & Probability Michigan State University East Lansing Michigan 48824 USA Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

We introduce a machine-learning-based framework for constructing continuum a non-Newtonian fluid dynamics model directly from a microscale description. Dumbbell polymer solutions are used as examples to demonstrate the essential ideas. To faithfully retain molecular fidelity, we establish a micro-macro correspondence via a set of encoders for the microscale polymer configurations and their macroscale counterparts, a set of nonlinear conformation tensors. The dynamics of these conformation tensors can be derived from the microscale model, and the relevant terms can be parametrized using machine learning. The final model, named the deep non-Newtonian model (DeePN2), takes the form of conventional non-Newtonian fluid dynamics models, with a generalized form of the objective tensor derivative that retains the microscale interpretations. Both the formulation of the dynamic equation and the neural network representation rigorously preserve the rotational invariance, which ensures the admissibility of the constructed model. Numerical results demonstrate the accuracy of DeePN2 where models based on empirical closures show limitations.

关键词： Learning Neuronal networks Complex fluids Non-Newtonian fluids Rheology Viscoelasticity Multiscale modeling

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Efficient sampling of high-dimensional free energy landscapes using adaptive reinforced dynamics

arXiv

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arXiv 2021年

作者： Wang, Dongdong Zhang, Linfeng Wang, Yanze Chang, Junhan Wang, Han Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States DP Technology Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Laboratory of Computational Physics Institute of Applied Physics and Computational Mathematics Fenghao East Road 2 Beijing100094 China School of Mathematical Sciences Peking University Beijing China Department of Mathematics Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Beijing Institute of Big Data Research Beijing100871 China

Enhanced sampling methods such as metadynamics and umbrella sampling have become essential tools for exploring the configuration space of molecules and materials. At the same time, they have long faced a number of issues such as the inefficiency when dealing with a large number of collective variables (CVs) or systems with high free energy barriers. In this work, we show that with the clustering and adaptive tuning techniques, the reinforced dynamics (RiD) scheme can be used to efficiently explore the configuration space and free energy landscapes with a large number of CVs or systems with high free energy barriers. We illustrate this by studying various representative and challenging examples. Firstly we demonstrate the efficiency of adaptive RiD compared with other methods, and construct the 9-dimensional free energy landscape of peptoid trimer which has energy barriers of more than 8 kcal/mol. We then study the folding of the protein chignolin using 18 CVs. In this case, both the folding and unfolding rates are observed to be equal to 4.30 µs−1. Finally, we propose a protein structure refinement protocol based on RiD. This protocol allows us to efficiently employ more than 100 CVs for exploring the landscape of protein structures and it gives rise to an overall improvement of 14.6 units over the initial Global Distance Test-High Accuracy (GDT-HA) score. © 2021, CC BY.

关键词： Wave functions

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Unbiased Estimation using a Class of Diffusion Processes

arXiv

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arXiv 2022年

作者： Ruzayqat, Hamza Beskos, Alexandros Crisan, Dan Jasra, Ajay Kantas, Nikolas Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 KSA Saudi Arabia Department of Statistical Science University College London LondonWC1E 6BT United Kingdom Department of Mathematics Imperial College London LondonSW7 2AZ United Kingdom

We study the problem of unbiased estimation of expectations with respect to (w.r.t.) π a given, general probability measure on (d, B(d)) that is absolutely continuous with respect to a standard Gaussian measure. We focus on simulation associated to a particular class of diffusion processes, sometimes termed the Schrödinger-Föllmer Sampler, which is a simulation technique that approximates the law of a particular diffusion bridge process {Xt}tϵ[0,1]on d, d ϵ 0. This latter process is constructed such that, starting at X0= 0, one has X1∼ π. Typically, the drift of the diffusion is intractable and, even if it were not, exact sampling of the associated diffusion is not possible. As a result, [10, 16] consider a stochastic Euler-Maruyama scheme that allows the development of biased estimators for expectations w.r.t. π. We show that for this methodology to achieve a mean square error of O(ϵ2), for arbitrary ϵ > 0, the associated cost is O(ϵ-5). We then introduce an alternative approach that provides unbiased estimates of expectations w.r.t. π, that is, it does not suffer from the time discretization bias or the bias related with the approximation of the drift function. We prove that to achieve a mean square error of O(ϵ2), the associated cost (which is random) is, with high probability, O(ϵ-2| log(ϵ)|2+δ), for any δ > 0. We implement our method on several examples including Bayesian inverse *** Codes 60J60, 62D05, 65C40 © 2022, CC BY.

关键词： Diffusion

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Local Order Metrics for Two-Phase Media Across Length Scales

arXiv

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arXiv 2022年

作者： Torquato, Salvatore Skolnick, Murray Kim, Jaeuk Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Chemistry Princeton University PrincetonNJ08544 United States McKetta Department of Chemical Engineering University of Texas at Austin AustinTX78712 United States

The capacity to devise order metrics for microstructures of multiphase heterogeneous media is a highly challenging task, given the richness of the possible geometries and topologies of the phases that can arise. This investigation initiates a program to formulate order metrics to characterize the degree of order/disorder of the microstructures of two-phase media in d-dimensional Euclidean space Rd across length scales. In particular, we propose the use of the local volume-fraction variance σV2 (R) associated with a spherical window of radius R as an order metric. We determine σV2 (R) as a function of R for 22 different models across the first three space dimensions, including both hyperuniform and nonhyperuniform systems with varying degrees of short- and long-range order. We find that the local volume-fraction variance as well as asymptotic coefficients and integral measures derived from it provide reasonably robust and sensitive order metrics to categorize disordered and ordered two-phase media across all length scales. © 2022, CC BY-SA.

关键词： Volume fraction

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Artificial neural network approach for turbulence models: A local framework

arXiv

引用

arXiv 2021年

作者： Xie, Chenyue Xiong, Xiangming Wang, Jianchun Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Mechanics and Aerospace Engineering Southern University of Science and Technology Shenzhen518055 China

A local artificial neural network (LANN) framework is developed for turbulence modeling. The Reynolds-averaged Navier-Stokes (RANS) unclosed terms are reconstructed by artificial neural network (ANN) based on the local coordinate system which is orthogonal to the curved walls. We verify the proposed model for the flows over periodic hills. The correlation coefficients of the RANS unclosed terms predicted by the LANN model can be made larger than 0.96 in an a priori analysis, and the relative error of the unclosed terms can be made smaller than 18%. In an a posteriori analysis, detailed comparisons are made on the results of RANS simulations using the LANN and Spalart-Allmaras (SA) models. It is shown that the LANN model performs better than the SA model in the prediction of the average velocity, wall-shear stress and average pressure, which gives the results that are essentially indistinguishable from the direct numerical simulation (DNS) data. The LANN model trained in low Reynolds number Re = 2800 can be directly applied in the cases of high Reynolds numbers Re = 5600, 10595, 19000, 37000 with accurate predictions. Furthermore, the LANN model is verified for flows over periodic hills with varying slopes. These results suggest that the LANN framework has a great potential to be applied to complex turbulent flows with curved *** Codes 76F40, 76F55, 76N99 Copyright © 2021, The Authors. All rights reserved.

关键词： Neural networks

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Flagellum Pumping Efficiency in Shear-Thinning Viscoelastic Fluids

arXiv

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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

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

arXiv

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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

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