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arXiv 2019年

作者： Babaei, Hasan Guo, Ruiqiang Hashemi, Amirreza Lee, Sangyeop Department of Mechanical Engineering and Materials Science University of Pittsburgh PittsburghPA15261 United States Department of Computational Modeling and Simulation University of Pittsburgh PittsburghPA15261 United States Department of Physics and Astronomy University of Pittsburgh PittsburghPA15261 United States

We report that single interatomic potential, developed using Gaussian regression of density functional theory calculation data, has high accuracy and flexibility to describe phonon transport with ab initio accuracy in two different atomistic configurations: perfect crystalline Si and crystalline Si with vacancies. The high accuracy of second- and third-order force constants from the Gaussian approximation potential (GAP) are demonstrated with phonon dispersion, Grüneisen parameter, three-phonon scattering rate, phonon-vacancy scattering rate, and thermal conductivity, all of which are very close to the results from density functional theory calculation. We also show that the widely used empirical potentials (Stillinger-Weber and Tersoff) produce much larger errors compared to the GAP. The computational cost of GAP is higher than the two empirical potentials, but five orders of magnitude lower than the density functional theory calculation. Our work shows that GAP can provide a new opportunity for studying phonon transport in partially disordered crystalline phases with the high predictive power of ab initio calculation but at a feasible computational cost. Copyright © 2019, The Authors. All rights reserved.

关键词： Phonons

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Accuracy control for large-eddy simulation of turbulent mixing - Integral length-scale approach 11

Accuracy control for large-eddy simulation of turbulent mixi...

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11th International Symposium on Turbulence and Shear Flow Phenomena, TSFP 2019

作者： Geurts, B.J. Rouhi, A. Piomelli, U. Multiscale Modeling and Simulation Faculty EEMCS University of Twente P.O. Box 517 Enschede7500 AE Netherlands Multiscale Physics of Energy Systems Center for Computational Energy Research Faculty of Applied Physics Eindhoven University of Technology P.O. Box 213 Eindhoven5600 MB Netherlands Department of Mechanical and Materials Engineering Queen’s University KingstonONK7L 4L9 Canada Department of Mechanical Engineering University of Melbourne Victoria3010 Australia

Turbulent flow at high Reynolds numbers is currently not accessible on the basis of direct numerical simulation (DNS) of the Navier-Stokes equations - the computational complexity is too high to allow DNS in most realistic flow conditions. Instead, Large-Eddy simulation (LES) offers an alternative in which the focus is on capturing the larger dynamic scales of a problem. However, the fundamental closure problem in LES induced by spatial filtering of nonlinear terms, and the role of discretization errors in the numerical treatment of the LES equations, induce a principal uncertainty in any LES prediction. This uncertainty requires quantification and control. We investigate error control capabilities of the Integral Length-Scale Approximation (ILSA) and apply this modeling to transitional and turbulent mixing, focussing on the achieved reliability of LES as function of the grid resolution and ‘sub-filter activity’. © 2019 International Symposium on Turbulence and Shear Flow Phenomena, TSFP. All rights reserved.

关键词： Large eddy simulation

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Right Ventricular Myocardial Mechanics: Multi-Modal Deformation, Microstructure, and modeling

SSRN

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SSRN 2020年

作者： Kakaletsis, Sotirios Meador, William D. Mathur, Mrudang Sugerman, Gabriella P. Jazwiec, Tomasz Malinowski, Marcin Lejeune, Emma Timek, Tomasz A. Rausch, Manuel K. Department of Biomedical Engineering The University of Texas at Austin AustinTX78712 United States Department of Aerospace Engineering and Engineering Mechanics The University of Texas at Austin AustinTX78712 United States Department of Mechanical Engineering The University of Texas at Austin AustinTX78712 United States Cardiothoracic Surgery Spectrum Health Grand RapidsMI49503 United States Department of Cardiac Vascular and Endovascular Surgery and Transplantology Medical University of Silesia School of Medicine in Katowice Silesian Centre for Heart Diseases Zabrze Poland Department of Cardiac Surgery Medical University of Silesia School of Medicine in Katowice Katowice Poland James T. Willerson Center for Cardiovascular Modeling and Simulation Oden Institute for Computational Engineering and Sciences The University of Texas at Austin AustinTX78712 United States

The right ventricular myocardium, much like the rest of the right side of the heart, has been consistently understudied. Presently, little is known about its mechanics, its microstructure, and its constitutive behavior. In this work, we set out to provide the first data on the mechanics of the right ventricular myocardium in both simple shear and uniaxial loading. To this end, we tested ovine tissue samples under a comprehensive mechanical testing protocol that consisted of six simple shear modes and three tension/compression modes. After mechanical testing, we conducted a histology-based microstructural analysis on each sample that yielded high resolution fiber distribution maps across the entire sample thickness. Equipped with this detailed mechanical and histological data, we employed an inverse finite element framework to determine the optimal form and parameters for microstructure-based constitutive models. The results of our study show that right ventricular myocardium exhibits nonlinear, anisotropic, tension/compression asymmetric behavior with negative Poynting effect and minimal hysteresis. In addition, we found that myocardial fibers changes angles transmurally and are dispersed within the fiber-sheet direction. Through our inverse finite element analysis, we found that the Holzapfel model successfully fits these data, even when selectively informed by rudimentary microstructural information. And, we found that the inclusion of higher-fidelity microstructural data improved the Holzapfel model's predictive ability. Looking forward, this investigation is a critical step towards understanding the fundamental mechanical behavior of right ventricular myocardium, and lays the groundwork for future whole-organ mechanical simulations. © 2020, The Authors. All rights reserved.

关键词： Anisotropy

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Data retrieval from building information models based on visual programming

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Visualization in engineering 2017年第1期5卷 1-14页

作者： Preidel, Cornelius Daum, Simon Borrmann, André Chair of Computational Modeling and Simulation TUM Department of Civil Geo and Environmental Engineering Arcisstraße Munich 2180333 Germany

Background: With the rising adoption of Building Information modeling (BIM) in the AEC sector, computational models supersede traditional ways of information provision based on textual documents and two-dimensional drawings. The use of models enables the streamlining of workflows, and the included virtual construction increases the quality of the final product, the building. To create a comprehensive description of a planned building, information from different sources must be combined, specified and regularly updated by the project’s stakeholders. The emerging models are highly structured, and instance files entail large amounts of data. However, in an unprocessed state, these models are of limited suitability for performing engineering tasks as the amount and structure does not match the domain-specific and purpose-oriented views. Methods: Selection and filtering data for the user’s needs is a well-understood task in computer science, and various approaches are available. A promising approach is the usage of formal query languages. In this paper, selected common query languages are examined and assessed for processing building model information. Based on the analysis, we come to the conclusion that textual query languages are too complex to be employed by typical end users in the construction industry such as architects and engineers. Results: To overcome this issue, two Visual Programming Languages representing a new, more intuitive mechanism for data retrieval are introduced. The first one, QL4BIM, is designed for general filtering of IFC models, the second one, VCCL, has been developed for Code Compliance Checking. Both languages provide operators based on the Relational Algebra to allow handling of relations - a highly required feature of BIM QLs. Conclusions: The paper concludes with a discussion of the strengths and limitations of visual programming languages in the BIM context. © 2017, The Author(s).

关键词： Building information modeling Information retrieval Relational algebra Visual programming

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Nonmonotonic Scission and Branching Free Energies as Functions of Hydrotrope Concentration for Charged Micelles

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Physical Review Letters 2018年第3期121卷 038001-038001页

作者： Taraknath Mandal Peter H. Koenig Ronald G. Larson Department of Chemical Engineering University of Michigan Ann Arbor Michigan 48109 USA Computational Chemistry Modeling and Simulation The Procter & Gamble Company 8611 Beckett Road West Chester Ohio 45069 USA

Using coarse-grained molecular dynamics simulations and an umbrella sampling method that uses local surfactant density as a reaction coordinate, we directly calculate, for the first time, both the scission and branching free energies of a model charged micelle [cationic cetyltrimethylammonium chloride (CTAC)] in the presence of inorganic and organic salts (hydrotropes). We find that while inorganic salt only weakly affects the micelle scission energy, organic hydrotropes produce a strong, nonmonotonic dependence of both scission energy and branching on salt concentration. The nonmonotonicity in scission energy is traced to a competition between electrostatic screening of the repulsions among the surfactant head groups and thinning of the micellar core, which result from attachment of the hydrotropes to the micelle surface. We are able to correlate the nonmonotonicity in the scission energy of CTAC micelles with the peak observed experimentally in viscosity versus hydrotrope concentration and the location of this peak in CTAC solutions.

关键词： Aggregation Self-assembly Aggregates Micelles Surfactants, micelles & vesicles Coarse graining computational complexity

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Ab initio phonon transport across grain boundaries in graphene using machine learning based on small dataset

arXiv

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arXiv 2019年

作者： Hashemi, Amirreza Guo, Ruiqiang Esfarjani, Keivan Lee, Sangyeop Computational Modeling and Simulation Program University of Pittsburgh PittsburghPA15261 United States Department of Mechanical Engineering and Materials Science University of Pittsburgh PittsburghPA15261 United States Department of Mechanical and Aerospace Engineering University of Virginia CharlottesvilleVA22904 United States Department of Materials Science and Engineering University of Virginia CharlottesvilleVA22904 United States Department of Physics University of Virginia CharlottesvilleVA22904 United States Department of Physics and Astronomy University of Pittsburgh PittsburghPA15261 United States

Establishing the structure-property relationship for grain boundaries (GBs) is critical for developing next generation functional materials, but has been severely hampered due to its extremely large configurational space. Atomistic simulations with low computational cost and high predictive power are strongly desirable, but the conventional simulations using empirical interatomic potentials and density functional theory suffer from the lack of predictive power and high computational cost, respectively. A machine learning interatomic potential (MLIP) recently emerged but often requires an extensive size of the training dataset, making it a less feasible approach. Here we demonstrate that an MLIP trained with a rationally designed small training dataset can predict thermal transport across GBs in graphene with ab initio accuracy at an affordable computational cost. In particular, we employed a rational approach based on the structural unit model to find a small set of GBs that can represent the entire configurational space and thus can serve as a cost-effective training dataset for the MLIP. Only 5 GBs were found to be enough to represent the entire configurational space of graphene GBs. Using the atomistic Green's function approach and the MLIP, we revealed that the structure-thermal resistance relation in graphene does not follow the common understanding that large dislocation density causes larger thermal resistance. In fact, thermal resistance is nearly independent of dislocation density at room temperature and is higher when the dislocation density is small at sub-room temperature. We explain this intriguing behavior with the buckling near a GB causing a strong scattering of flexural phonon modes. Our work shows that a machine learning technique combined with conventional wisdom (e.g., structural unit model) can extend the recent success of ab initio thermal transport simulation, which has been mostly limited to single crystals, to complex yet practically importa

关键词： Grain boundaries

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A general-purpose hierarchical mesh partitioning method with node balancing strategies for large-scale numerical simulations

arXiv

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arXiv 2018年

作者： Kong, Fande Stogner, Roy H. Gaston, Derek R. Peterson, John W. Permann, Cody J. Slaughter, Andrew E. Martineau, Richard C. Department of Modeling and Simulation Idaho National Laboratory Idaho FallsID United States Institute for Computational and Engineering Sciences University of Texas AustinTX United States

Large-scale parallel numerical simulations are essential for a wide range of engineering problems that involve complex, coupled physical processes interacting across a broad range of spatial and temporal scales. The data structures involved in such simulations (meshes, sparse matrices, etc.) are frequently represented as graphs, and these graphs must be optimally partitioned across the available computational resources in order for the underlying calculations to scale efficiently. Partitions which minimize the number of graph edges that are cut (edge-cuts) while simultaneously maintaining a balance in the amount of work (i.e. graph nodes) assigned to each processor core are desirable, and the performance of most existing partitioning software begins to degrade in this metric for partitions with more than than O(103) processor cores. In this work, we consider a general-purpose hierarchical partitioner which takes into account the existence of multiple processor cores and shared memory in a compute node while partitioning a graph into an arbitrary number of subgraphs. We demonstrate that our algorithms significantly improve the preconditioning efficiency and overall performance of realistic numerical simulations running on up to 32,768 processor cores with nearly 109 unknowns. Copyright © 2018, The Authors. All rights reserved.

关键词： Numerical models

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Proposed unified discrete event simulation content roadmap for M&S curricula

Proposed unified discrete event simulation content roadmap f...

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2017 Winter simulation Conference, WSC 2017

作者： Leathrum, James F. Mielke, Roland R. Collins, Andrew J. Audette, Michel A. Department of Modeling Simulation and Visualization Engineering Old Dominion University 1300 Engineering and Computational Sciences Building NorfolkVA23529 United States

ISBN: (纸本)9781538634288

This paper presents a new educational roadmap for teaching discrete event system (DES) simulation software design. This roadmap represents the hierarchical structure and inter-relationships characterizing the worldviews of DES simulation, namely, event scheduling and process interaction. The roadmap was developed from the authors' experience while teaching DES simulation to both undergraduate and graduate students, spanning several years. The roadmap's development was motivated by the need to strive for greater completeness as well as fewer inconsistencies in the material curriculum. The commonality between the worldviews is highlighted in striving for a uniform approach. The intent of this paper is to provide other educators a foundation for their own DES simulation course development. A simple example is used to illustrate the worldviews within the roadmap. © 2017 IEEE.

关键词： Curricula

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Screw dislocation structure and mobility in body centered cubic Fe predicted by a Gaussian Approximation Potential

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npj computational Materials 2018年第1期4卷 90-96页

作者： Francesco Maresca Daniele Dragoni Gábor Csányi Nicola Marzari William A.Curtin Laboratory for Multiscale Mechanics Modeling(LAMMM) Institute of Mechanical EngineeringÉcole Polytechnique Fédérale de LausanneLausanne CH-1015Switzerland Theory and Simulation of Materials(THEOS) and National Centre for Computational Design and Discovery of Novel Materials(NCCR MARVEL)École Polytechnique Fédérale de LausanneLausanne CH-1015Switzerland Dipartimento di Scienza dei Materiali Universitàdi Milano-BicoccaVia R.Cozzi 55Milan I-20125Italy Department of Engineering University of CambridgeTrumpington StreetCambridge CB21PZUK

The plastic flow behavior of bcc transition metals up to moderate temperatures is dominated by the thermally activated glide of screw dislocations,which in turn is determined by the atomic-scale screw dislocation core structure and the associated kink-pair nucleation mechanism for *** complex plasticity phenomena requires the simulation of many atoms and interacting dislocations and *** sizes are beyond the scope of first-principles methods and thus require empirical interatomic *** for the technological important case of bcc Fe,existing empirical interatomic potentials yield spurious ***,the structure and motion of the screw dislocations in Fe are studied using a new Gaussian Approximation Potential(GAP)for bcc Fe,which has been shown to reproduce the potential energy surface predicted by density-functional theory(DFT)and many associated *** Fe GAP predicts a compact,non-degenerate core structure,a single-hump Peierls potential,and glide on{110},consistent with DFT *** thermally activated motion at finite temperatures occurs by the expected kink-pair nucleation and propagation *** stress-dependent enthalpy barrier for screw motion,computed using the nudgedelastic-band method,follows closely a form predicted by standard theories with a zero-stress barrier of~1 eV,close to the experimental value of 0.84 eV,and a Peierls stress of~2 GPa consistent with DFT predictions of the Peierls potential.

关键词： structure dislocation cubic

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Quantifying Heart Valve Interstitial Cell Contractile State Using Highly Tunable Poly(Ethylene Glycol) Hydrogels

SSRN

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SSRN 2019年

作者： Khang, Alex Rodriguez, Andrea Gonzalez Schroeder, Megan E. Sansom, Jacob Lejeune, Emma Anseth, Kristi S. Sacks, Michael S. James T. Willerson Center for Cardiovascular Modeling and Simulation The Oden Institute for Computational Engineering and Sciences The Department of Biomedical Engineering The University of Texas at Austin 240 East 24th Street AustinTX78731 United States Department of Chemical and Biological Engineering University of Colorado at Boulder 3415 Colorado Avenue BoulderCO80309 United States Department of Materials Science and Engineering University of Colorado at Boulder 3415 Colorado Avenue BoulderCO80309 United States Biofrontiers Institute University of Colorado at Boulder 3415 Colorado Avenue BoulderCO80309 United States

Valve interstitial cells (VIC) are the primary cell type residing within heart valve tissues. In many valve pathologies, VICs become activated and will subsequently profoundly remodel the valve tissue extracellular matrix (ECM). A primary indicator of VIC activation is the upregulation of α-smooth muscle actin (αSMA) fibers, which in turn increase VIC contractility. Thus, contractile state reflects VIC activation and ECM biosynthesis levels. In general, cell contraction studies have largely utilized two-dimensional substrates,which are a vastly different mechanical environment than native tissues. To address this limitation, hydrogels have been a popular choice for studying cells in a three-dimensional environment due to their tunable properties and optical transparency, which allows for direct cell visualization. In the present study, we extended the use of hydrogels to study the active contractile behavior of VICs. Aortic VICs (AVIC) were encapsulated within poly(ethylene glycol) hydrogels and were subjected to flexural-deformation tests to assess the state of AVIC contraction. Using a finite element model of the bending experiment, we determined the effective shear modulus of the constructs and observed an increase in bending stiffness as a result of AVIC active contraction. Results indicated that AVIC contraction has a more pronounced effect on macroscale properties in softer gels (72 ± 21% increase in shear moduli within 2.5 kPa gels) and is dependent upon the availability of adhesion sites (0.5-1 mM CRGDS). We were able to image AVICs directly within the hydrogel and observed a time-dependent decrease in volume (time constant τ = 3.04 min) when the AVICs were induced into a hypertensive state. Our results indicate that AVIC contraction is regulated by the stiffness of the hydrogel, as part of the larger AVIC-biomaterial interactions. This finding suggests that AVIC contractile state can be profoundly modulated through their local micro environment. Thus, hydro

关键词： Polyethylene glycols

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