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A dynamical model for the calcineurin-NFATc signaling pathway and muscle fiber shifting

PAMM 2021年第1期20卷

作者： Yesid Villota-Narvaez Angélica Ramírez-Martínez Diego Garzón-Alvarado Oliver Röhrle Biomimetics Laboratory and Numerical Methods and Modeling Research Group (GNUM) Instituto de Biotecnología (IBUN) Universidad Nacional de Colombia Bogotá Colombia Stuttgart Centre for Simulation Sciences (SC SimTech) Pfaffenwaldring 5a 70569 Stuttgart Germany Computational modeling of natural systems Research Group (COMMONS) Mechanical Engineering Department Universidad Central Bogota Colombia Institute for Modeling and Simulation of Biomechanical Systems University of Stuttgart Pfaffenwaldring 5a 70569 Stuttgart Germany

Training exercise produces skeletal muscle adaptation: at the organ scale, as anatomical changes; and at the myofiber scale, as mitochondrial and protein type content. The protein content of a myofiber is controlled by the calcineurin-NFATc signaling pathway: exercise triggers the pathway, and its final product is the translocation of dephosphorylated NFATc to the nucleus. Once in the nucleus, NFATc controls the state of the gene program to encode the slow or the fast fiber type characteristics. In the long term, the adaptation of the fiber type characteristics produces a shift in muscle fiber type: an increase in the number of myofibers of the fast type (which means that myofibers of the slow type shift to fast type) is related to force production; and an increase in the number of myofibers of the slow type (myofibers of the fast type shift to slow type) is related to fatigue resistance. These macroscopic features, i.e. force production and fatigue resistance, are the main target of most training protocols; however, little attention is focused on the limitations imposed by the fiber distribution of muscles at the organ scale. Based on the calcineurin-NFATc signaling pathway, we represented an exercise stimulus by a cytosolic calcium signal, and simulated the dynamics of NFATc in the nucleus. In this contribution, we present a dynamical model for the calcineurin-NFATc signaling pathway to describe the time course of dephosphorilated NFATc in the nucleus. We used an experimental report of a continuous stimulation pattern for calibration, and an experimental report of a pulsed stimulation pattern for comparison; we obtained a good agreement between the simulations and the experimental measurements.

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Evaluation of a case study to design a BIM-based cycle planning concept 26

Evaluation of a case study to design a BIM-based cycle plann...

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26th Annual Conference of the International Group for Lean Construction: Evolving Lean Construction Towards Mature Production Management Across Cultures and Frontiers, IGLC 2018

作者： Häringer, Paul Borrmann, André Dept. for Civil Geo and Environmental Engineering Technical University of Munich Germany Department of Computational Modeling and Simulation Dept. for Civil Geo and Environmental Engineering Technical University of Munich Germany

ISBN: (纸本)9789380689296

Cycle Planning, or Takt Time Planning, is a key method to reduce the variability between different activities within the execution of a construction. A construction section such as a floor consists of multiple work zones, which should have continuous flow and similar cycle times to efficiently coordinate needed resources. However, for concrete structures it is often difficult to find suitable sizes of casting segments and their grouping to work zones. Nowadays, scheduling experts usually use their practical experience to find an intuitive solution for Cycle Planning, which might be sub-optimal. The objective of our research is thus to develop a semiautomatic method to generate optimal work zones for a cycle. The proposed solution is a BIM-based Cycle Planning concept for the cast in-situ construction method of walls. This paper lays the foundation for our concept and evaluates different designs of Cycle Planning layouts to ensure the practical relevance of the generated work zones. We provide an approach to the semiautomatic method: after splitting all wall objects into smaller sections, an optimization algorithm aggregates wall sections into casting segments and casting segments into work zones. © IGLC 2018 - Proceedings of the 26th Annual Conference of the International Group for Lean Construction: Evolving Lean Construction Towards Mature Production Management Across Cultures and Frontiers. All rights reserved.

关键词： Lean production

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Finite Cell Method for functionally graded materials based on V-models and homogenized microstructures

arXiv

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arXiv 2020年

作者： Wassermann, Benjamin Korshunova, Nina Kollmannsberger, Stefan Rank, Ernst Elber, Gershon Chair for Computation in Engineering Technical University of Munich Arcisstr. 21 München80333 Germany Chair of Computational Modeling and Simulation Technical University of Munich Arcisstr. 21 München80333 Germany Institute for Advanced Study Technical University of Munich Lichtenbergstr. 2a Garching85748 Germany Center for Graphics and Geometric Computing Technion Israel Institute of Technology Haifa3200003 Israel

This paper proposes an extension of the finite cell method (FCM) to V-rep models, a novel geometric framework for volumetric representations. This combination of an embedded domain approach (FCM) and a new modeling framework (V-rep) forms the basis for an efficient and accurate simulation of mechanical artifacts, which are not only characterized by complex shapes but also by their non-standard interior structure. These objects gain more and more interest in the context of the new design opportunities opened by additive manufacturing, mainly when graded or micro-structured material is applied. Two different types of functionally graded materials (FGM) are considered: The first one, multi-material FGM, is described using the V-rep models’ inherent property to assign different properties throughout the interior of a domain. The second, single-material FGM – which is heterogeneously micro-structured – characterizes the effective material behavior of representative volume elements by homogenization and performs large-scale simulations using the embedded domain approach. Copyright © 2020, The Authors. All rights reserved.

关键词： Functionally graded materials

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DeePMD-kit v2: A software package for Deep Potential models

arXiv

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arXiv 2023年

作者： Zeng, Jinzhe Zhang, Duo Lu, Denghui Mo, Pinghui Li, Zeyu Chen, Yixiao Rynik, Marián Huang, Li'ang Li, Ziyao Shi, Shaochen Wang, Yingze Ye, Haotian Tuo, Ping Yang, Jiabin Ding, Ye Li, Yifan Tisi, Davide Zeng, Qiyu Bao, Han Xia, Yu Huang, Jiameng Muraoka, Koki Wang, Yibo Chang, Junhan Yuan, Fengbo Bore, Sigbjørn Løland Cai, Chun Lin, Yinnian Wang, Bo Xu, Jiayan Zhu, Jia-Xin Luo, Chenxing Zhang, Yuzhi Goodall, Rhys E.A. Liang, Wenshuo Singh, Anurag Kumar Yao, Sikai Zhang, Jingchao Wentzcovitch, Renata Han, Jiequn Liu, Jie Jia, Weile York, Darrin M. Weinan, E. Car, Roberto Zhang, Linfeng Wang, Han Laboratory for Biomolecular Simulation Research Institute for Quantitative Biomedicine Department of Chemistry and Chemical Biology Rutgers University PiscatawayNJ08854 United States AI for Science Institute Beijing100080 China DP Technology Beijing100080 China Academy for Advanced Interdisciplinary Studies Peking University Beijing100871 China HEDPS CAPT College of Engineering Peking University Beijing100871 China College of Electrical and Information Engineering Hunan University Changsha China Yuanpei College Peking University Beijing100871 China Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Department of Experimental Physics Comenius University Mlynská Dolina F2 Bratislava842 48 Slovakia Center for Quantum Information Institute for Interdisciplinary Information Sciences Tsinghua University Beijing100084 China Center for Data Science Peking University Beijing100871 China ByteDance Research Zhonghang Plaza No. 43 North 3rd Ring West Road Haidian District Beijing China College of Chemistry and Molecular Engineering Peking University Beijing100871 China Baidu Inc. Beijing China Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University Zhejiang Hangzhou China Westlake AI Therapeutics Lab Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Hangzhou China Department of Chemistry Princeton University PrincetonNJ08544 United States SISSA Scuola Internazionale Superiore di Studi Avanzati Trieste34136 Italy Laboratory of Computational Science and Modeling Institute of Materials École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Department of Physics National University of Defense Technology Hunan Changsha410073 China State Key Lab of Processors Institute of Computing Technology Chinese Academy of Sciences Beijing China University of Chinese Academy of Sciences Beijing China School of Electronics Engineerin

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, Deep Potential - Range Correction (DPRc), Deep Potential Long Range (DPLR), GPU support for customized operators, model compression, non-von Neumann molecular dynamics (NVNMD), and improved usability, including documentation, compiled binary packages, graphical user interfaces (GUI), and application programming interfaces (API). This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, the article benchmarks the accuracy and efficiency of different models and discusses ongoing developments. © 2023, CC BY-NC-ND.

关键词： Molecular dynamics

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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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Machine-learning based interatomic potential for phonon transport in perfect crystalline Si and crystalline Si with vacancies

arXiv

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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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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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Theoretical analysis and simulation of phase separation in a driven bidirectional two-lane system

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Physical Review E 2019年第3期100卷 032133-032133页

作者： Qing-Yi Hao Rui Jiang Mao-Bin Hu Yunxin Zhang Chao-Yun Wu Ning Guo Key Laboratory of Modeling Simulation and Control of Complex Ecosystem in Dabie Mountains of Anhui Higher Education Institutes School of Mathematics and Computational Science Anqing Normal University Anqing 246133 China School of Mathematical Sciences Fudan University Shanghai 200433 China MOE Key Laboratory for Urban Transportation Complex Systems Theory and Technology Beijing Jiaotong University Beijing 100044 China School of Engineering Science University of Science and Technology of China Hefei 230026 China School of Automotive and Transportation Engineering Hefei University of Technology Hefei 230009 China

The two-lane driven system is a type of important model to research some transport systems, and also a powerful tool to investigate properties of nonequilibrium state systems. This paper presents a driven bidirectional two-lane model. The dynamic characteristics of the model with periodic boundary are investigated by Monte Carlo simulation, simple mean field, and cluster mean field methods, respectively. By simulations, phase separations are observed in the system with some values of model parameters. When the phase separation does not occur, cluster mean field results are in good agreement with simulation results. According to the cluster mean field analysis and simulations, a conjecture about the condition that the phase separation happens is proposed. Based on the conjecture, the phase boundary distinguishing phase separation state and homogeneous state is determined, and a corresponding phase diagram is drawn. The conjecture is validated through observing directly the spatiotemporal diagram and investigating the coarsening process of the system by simulation, and a possible mechanism causing the phase separation is also discussed. These outcomes maybe contribute to understand deeply transport systems including the congestion and efficiency of the transport, and enrich explorations of nonequilibrium state systems.

关键词： Dynamical phase transitions Phase diagrams Phase separation Phase transitions Transport phenomena

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