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arXiv 2021年

作者： Gosea, Ion Victor Gugercin, Serkan Unger, Benjamin Max Planck Institute for Dynamics of Complex Technical Systems Sandtorstr. 1 Magdeburg39106 Germany Department of Mathematics and Computational Modeling and Data Analytics Division Academy of Integrated Science VirginiaTech BlacksburgVA24061 United States SC Simulation Technology University of Stuttgart Germany

We present a novel projection-based model reduction framework for parametric linear time-invariant systems that allows interpolating the transfer function at a given frequency point along parameter-dependent curves as opposed to the standard approach where transfer function interpolation is achieved for a discrete set of parameter and frequency samples. We accomplish this goal by using parameter-dependent projection spaces. Our main result shows that for holomorphic system matrices, the corresponding interpolatory projection spaces are also holomorphic. The coefficients of the power series representation of the projection spaces can be computed iteratively using standard methods. We illustrate the analysis on three numerical *** Codes 93C05, 93C35, 32E30 Copyright © 2021, The Authors. All rights reserved.

关键词： Transfer functions

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Robotically Steered Needles: A Survey of Neurosurgical Applications and Technical Innovations

Robotic surgery (Auckland)

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Robotic surgery (Auckland) 2020年 7卷 1-23页

作者： Michel A Audette Stéphane P A Bordas Jason E Blatt Department of Computational Modeling and Simulation Engineering Old Dominion University Norfolk VA USA. Institute of Computational Engineering University of Luxembourg Faculty of Sciences Communication and Technology Esch-Sur-Alzette Luxembourg. Department of Neurosurgery University of Florida Gainesville FL USA.

This paper surveys both the clinical applications and main technical innovations related to steered needles, with an emphasis on neurosurgery. Technical innovations generally center on curvilinear robots that can adopt a complex path that circumvents critical structures and eloquent brain tissue. These advances include several needle-steering approaches, which consist of tip-based, lengthwise, base motion-driven, and tissue-centered steering strategies. This paper also describes foundational mathematical models for steering, where potential fields, nonholonomic bicycle-like models, spring models, and stochastic approaches are cited. In addition, practical path planning systems are also addressed, where we cite uncertainty modeling in path planning, intraoperative soft tissue shift estimation through imaging scans acquired during the procedure, and simulation-based prediction. Neurosurgical scenarios tend to emphasize straight needles so far, and span deep-brain stimulation (DBS), stereoelectroencephalography (SEEG), intracerebral drug delivery (IDD), stereotactic brain biopsy (SBB), stereotactic needle aspiration for hematoma, cysts and abscesses, and brachytherapy as well as thermal ablation of brain tumors and seizure-generating regions. We emphasize therapeutic considerations and complications that have been documented in conjunction with these applications.

关键词： brain biopsy brachytherapy deep-brain stimulation intracerebral drug delivery needle steering stereoelectroencephalography stereotactic needle aspiration

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“Surgical Gps” Proof of Concept for Scoliosis Surgery

“Surgical Gps” Proof of Concept for Scoliosis Surgery

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Spring simulation Conference (SpringSim)

作者： Austin Tapp Michel Audette Electrical Computer & Biomedical Engineering Old Dominion University Norfolk VA USA Computational Modeling & Simulation Engineering Old Dominion University Norfolk VA USA

ISBN: (数字)9781565553705

ISBN: (纸本)9781728163642

Scoliotic deformities may be addressed with either anterior or posterior approaches for scoliosis correction procedures. While typically quite invasive, the impact of these operations may be reduced through the use of computer-assisted surgery. A combination of physician-designated anatomical landmarks and surgical ontologies allows for real-time intraoperative guidance during computer-assisted surgical interventions. Predetermined landmarks are labeled on an identical patient model, which seeks to encompass vertebrae, intervertebral disks, ligaments, and other soft tissues. The inclusion of this anatomy permits the consideration of hypothetical forces that are previously not well characterized in a patient-specific manner. Updated ontologies then suggest procedural directions throughout the surgical corridor, observing the positioning of both the physician and the anatomical landmarks of interest at the present moment. Merging patient-specific models, physician-designated landmarks, and ontologies to produce real-time recommendations magnifies the successful outcome of scoliosis correction through enhanced pre-surgical planning, reduced invasiveness, and shorted recovery time.

关键词： Solid modeling Surgery Ontologies Deformable models computational modeling Ligaments Finite element analysis

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Efficient implementation of atom-density representations

arXiv

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arXiv 2021年

作者： Musil, Félix Veit, Max Goscinski, Alexander Fraux, Guillaume Willatt, Michael J. Stricker, Markus Junge, Till Ceriotti, Michele Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Laboratory for Multiscale Mechanics Modeling Institute of Mechanical Engineering École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Interdisciplinary Centre for Advanced Materials Simulation Ruhr-University Bochum Universitätsstraße 150 Bochum44801 Germany

Physically-motivated and mathematically robust atom-centred representations of molecular structures are key to the success of modern atomistic machine learning (ML) methods. They lie at the foundation of a wide range of methods to predict the properties of both materials and molecules as well as to explore and visualize the chemical compound and configuration space. Recently, it has become clear that many of the most effective representations share a fundamental formal connection: that they can all be expressed as a discretization of n-body correlation functions of the local atom density, suggesting the opportunity of standardizing and, more importantly, optimizing the calculation of such representations. We present an implementation, named librascal, whose modular design lends itself both to developing refinements to the density-based formalism and to rapid prototyping for new developments of rotationally equivariant atomistic representations. As an example, we discuss SOAP features, perhaps the most widely used member of this family of representations, to show how the expansion of the local density can be optimized for any choice of radial basis set. We discuss the representation in the context of a kernel ridge regression model, commonly used with SOAP features, and analyze how the computational effort scales for each of the individual steps of the calculation. By applying data reduction techniques in feature space, we show how to further reduce the total computational cost by at up to a factor of 4 or 5 without affecting the model’s symmetry properties and without significantly impacting its accuracy. Copyright © 2021, The Authors. All rights reserved.

关键词： Atoms

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Matrix Stiffness Regulates Mechanotransduction and Vascular Network Formation of Hipsc-Derived Endothelial Progenitors Encapsulated in 3d Hydrogels

SSRN

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SSRN 2025年

作者： Han, Jiwan Halwachs, Kathleen West, Toni Larsen, Bryce Sacks, Michael S. Rosales, Adrianne M. Zoldan, Janet Department of Biomedical Engineering The University of Texas at Austin AustinTX United States Department of Chemical Engineering The University of Texas at Austin AustinTX United States James T. Willerson Center for Cardiovascular Modeling and Simulation The Oden Institute for Computational Engineering and Sciences AustinTX United States

The mechanical properties of the extracellular matrix (ECM), particularly stiffness, regulate endothelial progenitor responses during vascular development, yet their behavior in physiologically compliant matrices (10 kPa), our results emphasize that vascularization is not solely driven by the most mechanotransductive environment but rather by a balance of compliance, contractility, and cell-induced remodeling. These findings underscore the need to design hydrogels that provide sufficient mechanotransduction for endothelial maturation while maintaining compliance to support dynamic vascular morphogenesis. This work provides a mechanically tuned framework for optimizing microenvironments to balance endothelial differentiation and vascular network formation in tissue engineering and regenerative medicine. © 2025, The Authors. All rights reserved.

关键词： Endothelial cells

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First-principles determination of the phonon-point defect scattering and thermal transport due to fission products in ThO2

arXiv

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arXiv 2023年

作者： Malakkal, Linu Katre, Ankita Zhou, Shuxiang Jiang, Chao Hurley, David H. Marianetti, Chris A. Khafizov, Marat Computational Mechanics and Materials Department Idaho National Laboratory Idaho FallsID83415 United States Department of Scientific Computing Modeling and Simulation SP Pune University Pune411007 India Idaho National Laboratory Idaho FallsID83415 United States Department of Applied Physics and Applied Mathematics Columbia University 500 West 120th Street New YorkNY10027 United States Department of Mechanical and Aerospace Engineering The Ohio State University 201 West 19th Ave ColumbusOH43210 United States

This work presents the first-principles calculations of the lattice thermal conductivity degradation due to point defects in thorium dioxide using an iterative solution of the Peirels-Boltzmann transport equation. We have used the non-perturbative Green's function methodology to compute the phononpoint defect scattering rates that consider the local distortion around the point defect, including the mass difference changes, interatomic force constants, and structural relaxation near the point defects. The point defects considered in this work include the vacancy of thorium (VTh) and oxygen (VO), substitutions of helium (HeTh), krypton (KrTh), zirconium (ZrTh), iodine (ITh) and xenon (XeTh) in the thorium site, and the three different configurations of the Schottky defects. The results of the phonon-defect scattering rate reveal that, among all the considered intrinsic defects, the thorium vacancy and helium substitution in the thorium site scatter the phonon most due to the substantial changes in the force constant and structural distortions. The scattering of phonons due to the substitutional defects unveils that the zirconium atom scatters phonons the least, followed by xenon, iodine, krypton, and helium. This is contrary to the intuition that the scattering strength follows HeTh > KrTh > ZrTh > ITh > XeTh based on the mass difference. This striking difference in the zirconium phonon scattering is due to the local chemical environment changes. Zirconium is an electropositive element with valency similar to thorium and, therefore, can bond with the oxygen atoms, thus creating less force constant variance compared to iodine, an electronegative element, and the noble gases helium, xenon, and krypton. These results can serve as a benchmark for analytical models and help the engineering-scale modeling effort for nuclear design. © 2023, CC BY.

关键词： Boltzmann equation

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Fluorine intercalated graphene: Formation of a two-dimensional spin lattice through pseudoatomization

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Physical Review Materials 2020年第7期4卷 074411-074411页

作者： Shashi B. Mishra Satyesh K. Yadav D. G. Kanhere B. R. K. Nanda Condensed Matter Theory and Computational Lab Department of Physics IIT Madras Chennai 600036 India Department of Metallurgical and Materials Engineering IIT Madras Chennai 600036 India Centre for Modeling and Simulation Savitribai Phule Pune University Pune 411007 India

A suspended layer made up of ferromagnetically ordered spins could be created between two- monolayer or multilayer graphene through intercalation. Stability and electronic structure studies show that, when fluorine molecules are intercalated between two mono/multilayer graphene, their bonds get stretched enough (∼1.9–2.0Å) to weaken their molecular singlet eigenstate. Geometrically, these stretched molecules form a pseudoatomized fluorine layer by maintaining a van der Waals separation of ∼2.6Å from the adjacent carbon layers. As there is a significant charge transfer from the adjacent carbon layers to the fluorine layers, a mixture of triplet and doublet states stabilizes to induce local spin moments at each fluorine site and in turn form a suspended two-dimensional spin lattice. The spins of this lattice align ferromagnetically with nearest-neighbor coupling strength as large as ∼100meV. Our finite-temperature ab initio molecular dynamics study reveals that the intercalated system can be stabilized up to a temperature of 100 K with an average magnetic moment of ∼0.6μB/F. However, if the graphene layers can be held fixed, the room-temperature stability of such a system is feasible.

关键词： Electronic structure Magnetic interactions Magnetism Graphene Interfaces Two-dimensional electron system

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Optimization of Full-Core Reactor simulations on Summit

Optimization of Full-Core Reactor Simulations on Summit

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Supercomputing Conference

作者： Misun Min Yu-Hsiang Lan Paul Fischer Elia Merzari Stefan Kerkemeier Malachi Phillips Thilina Rathnayake April Novak Derek Gaston Noel Chalmers Tim Warburton Mathematics and Computer Science Argonne National Laboratory Lemont USA Computer Science University of Illinois Urbana USA Computer Science and Mechanical Science & Engineering University of Illinois Urbana USA Nuclear Engineering Penn State University Park USA Computational Science Argonne National Laboratory Lemont USA Modeling and Simulation Idaho National Laboratory Idaho Falls USA AMD Research Advanced Micro Devices Inc. Austin USA Mathematics Virginia Tech Blacksburg USA

ISBN: (纸本)9781665454452

Nek5000/RS, a highly-performant open-source spectral element code, has recently achieved an unprecedented milestone in the simulation of nuclear reactors: the first full core computational fluid dynamics simulations of reactor cores, including pebble beds with 352,625 pebbles and 98M spectral elements (51 billion gridpoints), advanced in less than 0.25 seconds per Navier-Stokes timestep. The authors present performance and optimization considerations necessary to achieve this milestone when running on all of Summit. These optimizations led to a fourfold reduction in time-to-solution, making it possible to perform high-fidelity simulations of a single flow-through time in less than six hours for a full reactor core under prototypical conditions.

关键词： Analytical models Uncertainty computational modeling Biological system modeling Predictive models Topology Thermal analysis

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Hopping-Transport Mechanism for Reconfigurable Logic in Disordered Dopant Networks

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Physical Review Applied 2022年第6期17卷 064025-064025页

作者： Henri Tertilt Jesse Bakker Marlon Becker Bram de Wilde Indrek Klanberg Bernard J. Geurts Wilfred G. van der Wiel Andreas Heuer Peter A. Bobbert Institut für physikalische Chemie Westfälische Wilhelms-Universität Münster Münster Germany NanoElectronics Group University of Twente Enschede Netherlands Multiscale Modeling and Simulation Group Faculty of Electrical Engineering Mathematics and Computer Science MESA+ Institute for Nanotechnology and Center for Brain-Inspired Nano Systems (BRAINS) University of Twente Enschede Netherlands Center for Computational Energy Research (CCER) Eindhoven University of Technology Netherlands Fachbereich Physik Westfälische Wilhelms-Universität Münster Münster Germany Department of Applied Physics Eindhoven University of Technology Netherlands

We present an atomic-scale mechanism based on variable-range hopping of interacting charges enabling reconfigurable logic in dopant network processing units. Kinetic Monte Carlo simulations of the hopping process show temperature-dependent current-voltage characteristics and artificially evolved basic Boolean logic gates in very good agreement with experiment. The simulations provide unique insights into the local electrostatic potential and current flow in the dopant network, showing subtle changes induced by control voltages that set the conditions for the logic operation. These insights will be crucial in the systematic further development of this burgeoning technology for unconventional computing. The establishment of the principles underlying the logic functionality of these devices encourages the exploration and utilization of the same principles in other materials and device geometries.

关键词： Doping effects Hopping transport Neuromorphic computing Devices for digital logic, storage & processing Disordered systems Doped semiconductors Genetic algorithm Monte Carlo methods

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Multi-Material, Approach-Guided, Controlled-Resolution Breast Meshing for Fe-Based Interactive Surgery simulation

Multi-Material, Approach-Guided, Controlled-Resolution Breas...

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Annual modeling and simulation Conference (ANNSIM)

作者： Motaz Alqaoud John Plemmons Eric Feliberti Krishnanand Kaipa Gabor Fichtinger Yiming Xiao Tanweer Rashid Michel Audette Biomedical Engineering Old Dominion University Norfolk VA USA Department of Radiology Eastern Virginia Medical School Norfolk VA USA Department of Surgery Eastern Virginia Medical School Norfolk VA USA Mechanical & Aerospace Engineering Old Dominion University Norfolk VA USA School of Computing Queen’s University Kingston ON Canada Computer Science & Software Engineering Concordia University Montreal QC Canada Neuroimage Analytics Laboratory University of Texas Health Science Center San Antonio TX USA Computational Modeling & Simulation Engineering Old Dominion University Norfolk VA USA

This paper proposes a guided, controlled resolution framework for 3D multi-material meshing. Using data from magnetic resonance (MR) images, we efficiently focused on demonstrating our framework for patient-specific breast cases. As a result, we can preserve the shared boundaries and enhance the resolution without negating the aspect of simulation computing time needed for finite element analysis (FEA). Our output is a high-quality volumetric mesh comprising 21K cells representing the three main parts for breast surgery simulation and planning, fat, fibroglandular (FGT), and tumor mass. Our approach combines three steps, surface meshing, surface mesh decimation, and generating a volumetric mesh. We showed experimental results for every stage and compared our final output to other literature, proving our method's efficiency in an accurate, simple, and high-quality presentation of a patient-specific breast meshing.

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