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Hong R, Zheng T, Marra V, Yang D, Liu JK. Multi-scale modelling of the epileptic brain: advantages of computational therapy exploration. J Neural Eng 2024; 21:021002. [PMID: 38621378 DOI: 10.1088/1741-2552/ad3eb4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/15/2024] [Indexed: 04/17/2024]
Abstract
Objective: Epilepsy is a complex disease spanning across multiple scales, from ion channels in neurons to neuronal circuits across the entire brain. Over the past decades, computational models have been used to describe the pathophysiological activity of the epileptic brain from different aspects. Traditionally, each computational model can aid in optimizing therapeutic interventions, therefore, providing a particular view to design strategies for treating epilepsy. As a result, most studies are concerned with generating specific models of the epileptic brain that can help us understand the certain machinery of the pathological state. Those specific models vary in complexity and biological accuracy, with system-level models often lacking biological details.Approach: Here, we review various types of computational model of epilepsy and discuss their potential for different therapeutic approaches and scenarios, including drug discovery, surgical strategies, brain stimulation, and seizure prediction. We propose that we need to consider an integrated approach with a unified modelling framework across multiple scales to understand the epileptic brain. Our proposal is based on the recent increase in computational power, which has opened up the possibility of unifying those specific epileptic models into simulations with an unprecedented level of detail.Main results: A multi-scale epilepsy model can bridge the gap between biologically detailed models, used to address molecular and cellular questions, and brain-wide models based on abstract models which can account for complex neurological and behavioural observations.Significance: With these efforts, we move toward the next generation of epileptic brain models capable of connecting cellular features, such as ion channel properties, with standard clinical measures such as seizure severity.
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Affiliation(s)
- Rongqi Hong
- School of Computer Science, Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
| | - Tingting Zheng
- School of Computer Science, Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
| | | | - Dongping Yang
- Research Centre for Frontier Fundamental Studies, Zhejiang Lab, Hangzhou, People's Republic of China
| | - Jian K Liu
- School of Computer Science, Centre for Human Brain Health, University of Birmingham, Birmingham, United Kingdom
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2
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Amini PM, Rouse I, Subbotina J, Lobaskin V. Multiscale modelling of biomolecular corona formation on metallic surfaces. Beilstein J Nanotechnol 2024; 15:215-229. [PMID: 38379931 PMCID: PMC10877083 DOI: 10.3762/bjnano.15.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/16/2024] [Indexed: 02/22/2024]
Abstract
In the realm of food industry, the choice of non-consumable materials used plays a crucial role in ensuring consumer safety and product quality. Aluminum is widely used in food packaging and food processing applications, including dairy products. However, the interaction between aluminum and milk content requires further investigation to understand its implications. In this work, we present the results of multiscale modelling of the interaction between various surfaces, that is (100), (110), and (111), of fcc aluminum with the most abundant milk proteins and lactose. Our approach combines atomistic molecular dynamics, a coarse-grained model of protein adsorption, and kinetic Monte Carlo simulations to predict the protein corona composition in the deposited milk layer on aluminum surfaces. We consider a simplified model of milk, which is composed of the six most abundant milk proteins found in natural cow milk and lactose, which is the most abundant sugar found in dairy. Through our study, we ranked selected proteins and lactose adsorption affinities based on their corresponding interaction strength with aluminum surfaces and predicted the content of the naturally forming biomolecular corona. Our comprehensive investigation sheds light on the implications of aluminum in food processing and packaging, particularly concerning its interaction with the most abundant milk proteins and lactose. By employing a multiscale modelling approach, we simulated the interaction between metallic aluminum surfaces and the proteins and lactose, considering different crystallographic orientations. The results of our study provide valuable insights into the mechanisms of lactose and protein deposition on aluminum surfaces, which can aid in the general understanding of protein corona formation.
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Affiliation(s)
| | - Ian Rouse
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Julia Subbotina
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vladimir Lobaskin
- School of Physics, University College Dublin, Belfield, Dublin 4, Ireland
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3
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Anderson C, Ntala C, Ozel A, Reuben RL, Chen Y. Computational homogenization of histological microstructures in human prostate tissue: Heterogeneity, anisotropy and tension-compression asymmetry. Int J Numer Method Biomed Eng 2023; 39:e3758. [PMID: 37477174 PMCID: PMC10909480 DOI: 10.1002/cnm.3758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 03/21/2023] [Accepted: 07/01/2023] [Indexed: 07/22/2023]
Abstract
Human prostatic tissue exhibits complex mechanical behaviour due to its multiphasic, heterogeneous nature, with hierarchical microstructures involving epithelial compartments, acinar lumens and stromal tissue all interconnected in complex networks. This study aims to establish a computational homogenization framework for quantifying the mechanical behaviour of prostate tissue, considering its multiphasic heterogeneous microstructures and the mechanical characteristics of tissue constituents. Representative tissue microstructure models were reconstructed from high-resolution histology images. Parametric studies on the mechanical properties of the tissue constituents, particularly the fibre-reinforced hyper-elasticity of the stromal tissue, were carried out to investigate their effects on the apparent tissue properties. These were then benchmarked against the experimental data reported in literature. Results showed significant anisotropy, both structural and mechanical, and tension-compression asymmetry of the apparent behaviours of the prostatic tissue. Strong correlation with the key microstructural indices such as area fractions of tissue constituents and the tissue fabric tensor was also observed. The correlation between the stromal tissue orientation and the principal directions of the apparent properties suggested an essential role of stromal tissue in determining the directions of anisotropy and the compression-tension asymmetry characteristics in normal human prostatic tissue. This work presented a homogenization and histology-based computational approach to characterize the apparent mechanical behaviours of human prostatic or other similar glandular tissues, with the ultimate aim of assessing how pathological conditions (e.g., prostate cancer and benign prostatic hyperplasia) could affect the tissue mechanical properties in a future study.
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Affiliation(s)
- Calum Anderson
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
| | - Chara Ntala
- Department of Pathology, Western General HospitalUniversity of EdinburghEdinburghUK
| | - Ali Ozel
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
| | - Robert L. Reuben
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
| | - Yuhang Chen
- Institute of Mechanical, Process and Energy Engineering, School of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
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4
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Chahine Y, Magoon MJ, Maidu B, del Álamo JC, Boyle PM, Akoum N. Machine Learning and the Conundrum of Stroke Risk Prediction. Arrhythm Electrophysiol Rev 2023; 12:e07. [PMID: 37427297 PMCID: PMC10326666 DOI: 10.15420/aer.2022.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 02/07/2023] [Indexed: 07/11/2023] Open
Abstract
Stroke is a leading cause of death worldwide. With escalating healthcare costs, early non-invasive stroke risk stratification is vital. The current paradigm of stroke risk assessment and mitigation is focused on clinical risk factors and comorbidities. Standard algorithms predict risk using regression-based statistical associations, which, while useful and easy to use, have moderate predictive accuracy. This review summarises recent efforts to deploy machine learning (ML) to predict stroke risk and enrich the understanding of the mechanisms underlying stroke. The surveyed body of literature includes studies comparing ML algorithms with conventional statistical models for predicting cardiovascular disease and, in particular, different stroke subtypes. Another avenue of research explored is ML as a means of enriching multiscale computational modelling, which holds great promise for revealing thrombogenesis mechanisms. Overall, ML offers a new approach to stroke risk stratification that accounts for subtle physiologic variants between patients, potentially leading to more reliable and personalised predictions than standard regression-based statistical associations.
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Affiliation(s)
- Yaacoub Chahine
- Division of Cardiology, University of Washington, Seattle, WA, US
| | - Matthew J Magoon
- Department of Bioengineering, University of Washington, Seattle, WA, US
| | - Bahetihazi Maidu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, US
| | - Juan C del Álamo
- Department of Mechanical Engineering, University of Washington, Seattle, WA, US
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, US
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, US
| | - Patrick M Boyle
- Department of Bioengineering, University of Washington, Seattle, WA, US
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, US
- Center for Cardiovascular Biology, University of Washington, Seattle, WA, US
| | - Nazem Akoum
- Division of Cardiology, University of Washington, Seattle, WA, US
- Department of Bioengineering, University of Washington, Seattle, WA, US
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5
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Degond P, Manhart A, Merino-Aceituno S, Peurichard D, Sala L. How environment affects active particle swarms: a case study. R Soc Open Sci 2022; 9:220791. [PMID: 36533200 PMCID: PMC9748504 DOI: 10.1098/rsos.220791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
We investigate the collective motion of self-propelled agents in an environment filled with obstacles that are tethered to fixed positions via springs. The active particles are able to modify the environment by moving the obstacles through repulsion forces. This creates feedback interactions between the particles and the obstacles from which a breadth of patterns emerges (trails, band, clusters, honey-comb structures, etc.). We will focus on a discrete model first introduced in Aceves-Sanchez P et al. (2020, Bull. Math. Biol. 82, 125 (doi:10.1007/s11538-020-00805-z)), and derived into a continuum PDE model. As a first major novelty, we perform an in-depth investigation of pattern formation of the discrete and continuum models in two dimensions: we provide phase-diagrams and determine the key mechanisms for bifurcations to happen using linear stability analysis. As a result, we discover that the agent-agent repulsion, the agent-obstacle repulsion and the obstacle's spring stiffness are the key forces in the appearance of patterns, while alignment forces between the particles play a secondary role. The second major novelty lies in the development of an innovative methodology to compare discrete and continuum models that we apply here to perform an in-depth analysis of the agreement between the discrete and continuum models.
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Affiliation(s)
- Pierre Degond
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS, Toulouse Cedex 9 31062, France
| | - Angelika Manhart
- Mathematics Department, University College London, 25 Gordon Street, London, UK
| | - Sara Merino-Aceituno
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, Vienna 1090, Austria
| | - Diane Peurichard
- Inria, Laboratoire Jacques-Louis Lions, Sorbonne Université, CNRS, Université de Paris, 4, Place Jussieu, Paris Cedex 05 75252, France
| | - Lorenzo Sala
- INRIA Saclay Ile-de-France, 1 rue Honoré d’Estienne d’Orves, Palaiseau 91120, France
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6
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Abstract
Nonlinear differential equations rarely admit closed-form solutions, thus requiring numerical time-stepping algorithms to approximate solutions. Further, many systems characterized by multiscale physics exhibit dynamics over a vast range of timescales, making numerical integration expensive. In this work, we develop a hierarchy of deep neural network time-steppers to approximate the dynamical system flow map over a range of time-scales. The model is purely data-driven, enabling accurate and efficient numerical integration and forecasting. Similar ideas can be used to couple neural network-based models with classical numerical time-steppers. Our hierarchical time-stepping scheme provides advantages over current time-stepping algorithms, including (i) capturing a range of timescales, (ii) improved accuracy in comparison with leading neural network architectures, (iii) efficiency in long-time forecasting due to explicit training of slow time-scale dynamics, and (iv) a flexible framework that is parallelizable and may be integrated with standard numerical time-stepping algorithms. The method is demonstrated on numerous nonlinear dynamical systems, including the Van der Pol oscillator, the Lorenz system, the Kuramoto-Sivashinsky equation, and fluid flow pass a cylinder; audio and video signals are also explored. On the sequence generation examples, we benchmark our algorithm against state-of-the-art methods, such as LSTM, reservoir computing and clockwork RNN. This article is part of the theme issue 'Data-driven prediction in dynamical systems'.
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Affiliation(s)
- Yuying Liu
- Department of Applied Mathematics, University of Washington, Seattle, WA 98105, USA
| | - J. Nathan Kutz
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Steven L. Brunton
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98105, USA
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Alvin Wei Ze Chew, Limao Zhang. Data-driven multiscale modelling and analysis of COVID-19 spatiotemporal evolution using explainable AI. Sustain Cities Soc 2022; 80. [PMID: 35186668 DOI: 10.1016/j.scs.2022.103772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/27/2022] [Accepted: 02/10/2022] [Indexed: 05/21/2023]
Abstract
To quantificationally identify the optimal control measures for regulators to best minimize COVID-19′s growth (G-rate) and death (D-rate) rates in today's context, this paper develops a top-down multiscale engineering approach which encompasses a series of systematic analyses, namely: (global scale) predictive modelling of G-rate and D-rate due to COVID-19 globally, followed by determining the most effective control factors which can best minimize both parameters over time via explainable Artificial Intelligence (AI) with SHAP (SHapley Additive exPlanations) method; (continental scale) same predictive forecasting of G-rate and D-rate in all continents, followed by performing explainable SHAP analysis to determine the most effective control factors for the respective continents; and (country scale) clustering the different countries (> 150 in total) into 3 main clusters to identify the universal set of effective control measures. By using the historical period between 2 May 2020 and 1 Oct 2021, the average MAPE scores for forecasting G-rate and D-rate are within 10%, or less on average, at the global and continental scales. Systematically, we have quantificationally demonstrated that the top 3 most effective control measures for regulators to best minimize G-rate universally are COVID-CONTACT-TRACING, PUBLIC-GATHERING-RULES, and COVID-STRINGENCY-INDEX, while the control factors relating to D-rate depend on the modelling scenario.
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8
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Corti A, Colombo M, Rozowsky JM, Casarin S, He Y, Carbonaro D, Migliavacca F, Rodriguez Matas JF, Berceli SA, Chiastra C. A predictive multiscale model of in-stent restenosis in femoral arteries: linking haemodynamics and gene expression with an agent-based model of cellular dynamics. J R Soc Interface 2022; 19:20210871. [PMID: 35350882 PMCID: PMC8965415 DOI: 10.1098/rsif.2021.0871] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In-stent restenosis (ISR) is a maladaptive inflammatory-driven response of femoral arteries to percutaneous transluminal angioplasty and stent deployment, leading to lumen re-narrowing as consequence of excessive cellular proliferative and synthetic activities. A thorough understanding of the underlying mechanobiological factors contributing to ISR is still lacking. Computational multiscale models integrating both continuous- and agent-based approaches have been identified as promising tools to capture key aspects of the complex network of events encompassing molecular, cellular and tissue response to the intervention. In this regard, this work presents a multiscale framework integrating the effects of local haemodynamics and monocyte gene expression data on cellular dynamics to simulate ISR mechanobiological processes in a patient-specific model of stented superficial femoral artery. The framework is based on the coupling of computational fluid dynamics simulations (haemodynamics module) with an agent-based model (ABM) of cellular activities (tissue remodelling module). Sensitivity analysis and surrogate modelling combined with genetic algorithm optimization were adopted to explore the model behaviour and calibrate the ABM parameters. The proposed framework successfully described the patient lumen area reduction from baseline to one-month follow-up, demonstrating the potential capabilities of this approach in predicting the short-term arterial response to the endovascular procedure.
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Affiliation(s)
- Anna Corti
- LaBS, Department of Chemistry, Materials and Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy
| | - Monika Colombo
- LaBS, Department of Chemistry, Materials and Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy.,Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zürich, Switzerland
| | - Jared M Rozowsky
- Department of Surgery, University of Florida, Gainesville, FL, USA
| | - Stefano Casarin
- Department of Surgery, Houston Methodist Hospital, Houston, TX, USA.,Center for Computational Surgery, Houston Methodist Research Institute, Houston, TX, USA.,Houston Methodist Academic Institute, Houston, TX, USA
| | - Yong He
- Department of Surgery, University of Florida, Gainesville, FL, USA
| | - Dario Carbonaro
- PoliToBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Francesco Migliavacca
- LaBS, Department of Chemistry, Materials and Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy
| | - Jose F Rodriguez Matas
- LaBS, Department of Chemistry, Materials and Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy
| | - Scott A Berceli
- Department of Surgery, University of Florida, Gainesville, FL, USA.,Malcom Randall VAMC, Gainesville, FL, USA
| | - Claudio Chiastra
- LaBS, Department of Chemistry, Materials and Chemical Engineering 'Giulio Natta', Politecnico di Milano, Milan, Italy.,PoliToBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
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9
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Krauklis AE, Karl CW, Rocha IBCM, Burlakovs J, Ozola-Davidane R, Gagani AI, Starkova O. Modelling of Environmental Ageing of Polymers and Polymer Composites-Modular and Multiscale Methods. Polymers (Basel) 2022; 14:216. [PMID: 35012240 PMCID: PMC8747293 DOI: 10.3390/polym14010216] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/29/2021] [Indexed: 12/04/2022] Open
Abstract
Service lifetimes of polymers and polymer composites are impacted by environmental ageing. The validation of new composites and their environmental durability involves costly testing programs, thus calling for more affordable and safe alternatives, and modelling is seen as such an alternative. The state-of-the-art models are systematized in this work. The review offers a comprehensive overview of the modular and multiscale modelling approaches. These approaches provide means to predict the environmental ageing and degradation of polymers and polymer composites. Furthermore, the systematization of methods and models presented herein leads to a deeper and reliable understanding of the physical and chemical principles of environmental ageing. As a result, it provides better confidence in the modelling methods for predicting the environmental durability of polymeric materials and fibre-reinforced composites.
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Affiliation(s)
- Andrey E. Krauklis
- Institute for Mechanics of Materials, University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia;
| | | | - Iuri B. C. M. Rocha
- Faculty of Civil Engineering and Geosciences, Delft University of Technology, P.O. Box 5048, 2600 GA Delft, The Netherlands;
| | - Juris Burlakovs
- Institute of Forestry and Rural Engineering, Estonian University of Life Sciences, 5 Kreutzwaldi St., 51014 Tartu, Estonia;
| | - Ruta Ozola-Davidane
- Faculty of Geography and Earth Sciences, University of Latvia, Raina Blvd 19, LV-1586 Riga, Latvia;
| | - Abedin I. Gagani
- Siemens Digital Industries Software, Via Werner von Siemens 1, 20128 Milan, Italy;
| | - Olesja Starkova
- Institute for Mechanics of Materials, University of Latvia, Jelgavas Street 3, LV-1004 Riga, Latvia;
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10
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Davidović A, Coudière Y, Bourgault Y. Modelling the action potential propagation in a heart with structural heterogeneities: From high-resolution MRI to numerical simulations. Int J Numer Method Biomed Eng 2021; 37:e3322. [PMID: 32052589 DOI: 10.1002/cnm.3322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 01/28/2020] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
Mathematical modelling and numerical simulation in cardiac electrophysiology have already been studied extensively. However, there is a clear lack of techniques and methodologies for studying the propagation of action potential in a heart with structural defects. In this article, we present a modified version of the bidomain model, derived using homogenisation techniques with the assumption of existence of diffusive inclusions in the cardiac tissue. The diffusive inclusions represent regions without electrically active myocytes, for example, fat, fibrosis, and so forth. We present an application of this model to a rat heart. Starting from high-resolution MRI, the geometry of the heart is built and meshed using image processing techniques. We perform a study of the effects of tissue heterogeneities induced by diffusive inclusions on the velocity and shape of the depolarisation wavefront. We present several test cases with different geometries of diffusive inclusions. We reach the conclusion that the conduction velocity is not affected in the best cases, while it is affected by up to 76% in the worst case scenario. Additionally, the shape of the wavefront was affected in some cases.
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Affiliation(s)
- Anđela Davidović
- Carmen Team, Inria Bordeaux-Sud-Ouest, Bordeaux, France
- Calcul scientifique et Modélisation, Institut de Mathématiques de Bordeaux, CNRS UMR 5251, Université de Bordeaux, Bordeaux, France
- L'Institut de RYthmologie et Modélisation Cardiaque-LIRYC, Bordeaux, France
- Department of Computational Biology, CNRS USR 3756, Institut Pasteur, Paris, France
| | - Yves Coudière
- Carmen Team, Inria Bordeaux-Sud-Ouest, Bordeaux, France
- Calcul scientifique et Modélisation, Institut de Mathématiques de Bordeaux, CNRS UMR 5251, Université de Bordeaux, Bordeaux, France
- L'Institut de RYthmologie et Modélisation Cardiaque-LIRYC, Bordeaux, France
| | - Yves Bourgault
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada
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11
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Luk OO, Lakhlili J, Hoenen O, von Toussaint U, Scott BD, Coster DP. Towards validated multiscale simulations for fusion. Philos Trans A Math Phys Eng Sci 2021; 379:20200074. [PMID: 33775143 DOI: 10.1098/rsta.2020.0074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Harnessing energy produced by thermonuclear fusion reactions has the potential to provide a clean and inexpensive source of energy to Earth. However, throughout the past seven decades, physicists learned that creating our very own fusion energy source is very difficult to achieve. We constructed a component-based, multiscale fusion workflow to model fusion plasma inside the core of a tokamak device. To ensure the simulation results agree with experimental values, the model needs to undergo the process of verification, validation and uncertainty quantification (VVUQ). This paper will go over the VVUQ work carried out in the multiscale fusion workflow (MFW), with the help of the EasyVVUQ software library developed by the VECMA project. In particular, similarity of distributions from simulation and experiment is explored as a validation metric. Such initial validation measures provide insights into the accuracy of the simulation results. This article is part of the theme issue 'Reliability and reproducibility in computational science: implementing verification, validation and uncertainty quantification in silico'.
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Affiliation(s)
- O O Luk
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - J Lakhlili
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - O Hoenen
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | | | - B D Scott
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - D P Coster
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
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12
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Di Pierro A, Mortazavi B, Noori H, Rabczuk T, Fina A. A Multiscale Investigation on the Thermal Transport in Polydimethylsiloxane Nanocomposites: Graphene vs. Borophene. Nanomaterials (Basel) 2021; 11:1252. [PMID: 34064564 DOI: 10.3390/nano11051252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 11/26/2022]
Abstract
Graphene and borophene are highly attractive two-dimensional materials with outstanding physical properties. In this study we employed combined atomistic continuum multi-scale modeling to explore the effective thermal conductivity of polymer nanocomposites made of polydimethylsiloxane (PDMS) polymer as the matrix and graphene and borophene as nanofillers. PDMS is a versatile polymer due to its chemical inertia, flexibility and a wide range of properties that can be tuned during synthesis. We first conducted classical Molecular Dynamics (MD) simulations to calculate the thermal conductance at the interfaces between graphene and PDMS and between borophene and PDMS. Acquired results confirm that the interfacial thermal conductance between nanosheets and polymer increases from the single-layer to multilayered nanosheets and finally converges, in the case of graphene, to about 30 MWm−2 K−1 and, for borophene, up to 33 MWm−2 K−1. The data provided by the atomistic simulations were then used in the Finite Element Method (FEM) simulations to evaluate the effective thermal conductivity of polymer nanocomposites at the continuum level. We explored the effects of nanofiller type, volume content, geometry aspect ratio and thickness on the nanocomposite effective thermal conductivity. As a very interesting finding, we found that borophene nanosheets, despite having almost two orders of magnitude lower thermal conductivity than graphene, can yield very close enhancement in the effective thermal conductivity in comparison with graphene, particularly for low volume content and small aspect ratios and thicknesses. We conclude that, for the polymer-based nanocomposites, significant improvement in the thermal conductivity can be reached by improving the bonding between the fillers and polymer, or in other words, by enhancing the thermal conductance at the interface. By taking into account the high electrical conductivity of borophene, our results suggest borophene nanosheets as promising nanofillers to simultaneously enhance the polymers’ thermal and electrical conductivity.
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13
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Purlis E, Cevoli C, Fabbri A. Modelling Volume Change and Deformation in Food Products/Processes: An Overview. Foods 2021; 10:778. [PMID: 33916418 PMCID: PMC8067021 DOI: 10.3390/foods10040778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/25/2022] Open
Abstract
Volume change and large deformation occur in different solid and semi-solid foods during processing, e.g., shrinkage of fruits and vegetables during drying and of meat during cooking, swelling of grains during hydration, and expansion of dough during baking and of snacks during extrusion and puffing. In addition, food is broken down during oral processing. Such phenomena are the result of complex and dynamic relationships between composition and structure of foods, and driving forces established by processes and operating conditions. In particular, water plays a key role as plasticizer, strongly influencing the state of amorphous materials via the glass transition and, thus, their mechanical properties. Therefore, it is important to improve the understanding about these complex phenomena and to develop useful prediction tools. For this aim, different modelling approaches have been applied in the food engineering field. The objective of this article is to provide a general (non-systematic) review of recent (2005-2021) and relevant works regarding the modelling and simulation of volume change and large deformation in various food products/processes. Empirical- and physics-based models are considered, as well as different driving forces for deformation, in order to identify common bottlenecks and challenges in food engineering applications.
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Affiliation(s)
| | - Chiara Cevoli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, Università di Bologna, 47521 Cesena, Italy;
| | - Angelo Fabbri
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, Università di Bologna, 47521 Cesena, Italy;
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14
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Yazdani A, Deng Y, Li H, Javadi E, Li Z, Jamali S, Lin C, Humphrey JD, Mantzoros CS, Em Karniadakis G. Integrating blood cell mechanics, platelet adhesive dynamics and coagulation cascade for modelling thrombus formation in normal and diabetic blood. J R Soc Interface 2021; 18:20200834. [PMID: 33530862 PMCID: PMC8086870 DOI: 10.1098/rsif.2020.0834] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 01/12/2021] [Indexed: 11/12/2022] Open
Abstract
Normal haemostasis is an important physiological mechanism that prevents excessive bleeding during trauma, whereas the pathological thrombosis especially in diabetics leads to increased incidence of heart attacks and strokes as well as peripheral vascular events. In this work, we propose a new multiscale framework that integrates seamlessly four key components of blood clotting, namely transport of coagulation factors, coagulation kinetics, blood cell mechanics and platelet adhesive dynamics, to model the development of thrombi under physiological and pathological conditions. We implement this framework to simulate platelet adhesion due to the exposure of tissue factor in a three-dimensional microchannel. Our results show that our model can simulate thrombin-mediated platelet activation in the flowing blood, resulting in platelet adhesion to the injury site of the channel wall. Furthermore, we simulate platelet adhesion in diabetic blood, and our results show that both the pathological alterations in the biomechanics of blood cells and changes in the amount of coagulation factors contribute to the excessive platelet adhesion and aggregation in diabetic blood. Taken together, this new framework can be used to probe synergistic mechanisms of thrombus formation under physiological and pathological conditions, and open new directions in modelling complex biological problems that involve several multiscale processes.
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Affiliation(s)
- Alireza Yazdani
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Yixiang Deng
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
- School of Engineering, Brown University, Providence, RI 02912, USA
| | - He Li
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Elahe Javadi
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA
| | - Zhen Li
- Department of Mechanical Engineering, Clemson University, Clemson, SC 29634, USA
| | - Safa Jamali
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA 02115, USA
| | - Chensen Lin
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Jay D. Humphrey
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Christos S. Mantzoros
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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15
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Kopač D, Jurković DL, Likozar B, Huš M. First-Principles-Based Multiscale Modelling of Nonoxidative Butane Dehydrogenation on Cr 2O 3(0001). ACS Catal 2020; 10:14732-14746. [PMID: 33362945 PMCID: PMC7754517 DOI: 10.1021/acscatal.0c03197] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/16/2020] [Indexed: 11/29/2022]
Abstract
Propane (C3H8) and butane (C4H10) are short straight-chain alkane molecules that are difficult to convert catalytically. Analogous to propane, butane can be dehydrogenated to butenes (also known as butylenes) or butadiene, which are used industrially as raw materials when synthesizing various chemicals (plastics, rubbers, etc.). In this study, we present results of detailed first-principles-based multiscale modelling of butane dehydrogenation, consisting of three size- and time-scales. The reaction is modelled over Cr2O3(0001) chromium oxide, which is commonly used in the industrial setting. A complete 108-step reaction pathway of butane (C4H10) dehydrogenation was studied, yielding 1-butene (CH2CHCH2CH3) and 2-butene (CH3CHCHCH3), 1-butyne (CHCCH2CH3) and 2-butyne (CH3CCCH3), butadiene (CH2CHCHCH2), butenyne (CH2CHCCH), and ultimately butadiyne (CHCCCH). We include cracking and coking reactions (yielding C1, C2, and C3 hydrocarbons) in the model to provide a thorough description of catalyst deactivation as a function of the temperature and time. Density functional theory calculations with the Hubbard U model were used to study the reaction on the atomistic scale, resulting in the complete energetics and first-principles kinetic parameters for the dehydrogenation reaction. They were cast in a kinetic model using mean-field microkinetics and kinetic Monte Carlo simulations. The former was used to obtain gas equilibrium conditions in the steady-state regime, which were fed in the latter to provide accurate surface kinetics. A full reactor simulation was used to account for the macroscopic properties of the catalytic particles: their loading, specific surface area, and density and reactor parameters: size, design, and feed gas flow. With this approach, we obtained first-principles estimates of the catalytic conversion, selectivity to products, and time dependence of the catalyst activity, which can be paralleled to experimental data. We show that 2-butene is the most abundant product of dehydrogenation, with selectivity above 90% and turn-over frequency above 10-3 s-1 at T = 900 K. Butane conversion is below 5% at such low temperature, but rises above 40% at T > 1100 K. Activity starts to drop after ∼6 h because of surface poisoning with carbon. We conclude that the dehydrogenation of butane is a viable alternative to conventional olefin production processes.
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Affiliation(s)
- Drejc Kopač
- Department
of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Damjan Lašič Jurković
- Department
of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Blaž Likozar
- Department
of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Matej Huš
- Department
of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
- Association
for Technical Culture of Slovenia (ZOTKS), SI-1000 Ljubljana, Slovenia
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16
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Abstract
The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.
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Affiliation(s)
- A Gheorghiu
- Centre for Computational Science, University College London, London, UK
| | - P V Coveney
- Centre for Computational Science, University College London, London, UK.,Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - A A Arabi
- Centre for Computational Science, University College London, London, UK.,College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates
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17
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Yates CA, George A, Jordana A, Smith CA, Duncan AB, Zygalakis KC. The blending region hybrid framework for the simulation of stochastic reaction-diffusion processes. J R Soc Interface 2020; 17:20200563. [PMID: 33081647 PMCID: PMC7653393 DOI: 10.1098/rsif.2020.0563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The simulation of stochastic reaction–diffusion systems using fine-grained representations can become computationally prohibitive when particle numbers become large. If particle numbers are sufficiently high then it may be possible to ignore stochastic fluctuations and use a more efficient coarse-grained simulation approach. Nevertheless, for multiscale systems which exhibit significant spatial variation in concentration, a coarse-grained approach may not be appropriate throughout the simulation domain. Such scenarios suggest a hybrid paradigm in which a computationally cheap, coarse-grained model is coupled to a more expensive, but more detailed fine-grained model, enabling the accurate simulation of the fine-scale dynamics at a reasonable computational cost. In this paper, in order to couple two representations of reaction–diffusion at distinct spatial scales, we allow them to overlap in a ‘blending region’. Both modelling paradigms provide a valid representation of the particle density in this region. From one end of the blending region to the other, control of the implementation of diffusion is passed from one modelling paradigm to another through the use of complementary ‘blending functions’ which scale up or down the contribution of each model to the overall diffusion. We establish the reliability of our novel hybrid paradigm by demonstrating its simulation on four exemplar reaction–diffusion scenarios.
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Affiliation(s)
- Christian A Yates
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Adam George
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Armand Jordana
- Centre de Mathématiques et de Leurs Applications, CNRS, ENS Paris-Saclay, Université Paris-Saclay, 94235 Cachan cedex, France
| | - Cameron A Smith
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Andrew B Duncan
- Department of Mathematics, Imperial College London, London SW7 2AZ, UK
| | - Konstantinos C Zygalakis
- School of Mathematics, University of Edinburgh, James Clerk Maxwell Building, The King's Buildings, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
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18
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Alsharif SA, Power D, Rouse I, Lobaskin V. In Silico Prediction of Protein Adsorption Energy on Titanium Dioxide and Gold Nanoparticles. Nanomaterials (Basel) 2020; 10:E1967. [PMID: 33020391 DOI: 10.3390/nano10101967] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/01/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023]
Abstract
The free energy of adsorption of proteins onto nanoparticles offers an insight into the biological activity of these particles in the body, but calculating these energies is challenging at the atomistic resolution. In addition, structural information of the proteins may not be readily available. In this work, we demonstrate how information about adsorption affinity of proteins onto nanoparticles can be obtained from first principles with minimum experimental input. We use a multiscale model of protein-nanoparticle interaction to evaluate adsorption energies for a set of 59 human blood serum proteins on gold and titanium dioxide (anatase) nanoparticles of various sizes. For each protein, we compare the results for 3D structures derived from experiments to those predicted computationally from amino acid sequences using the I-TASSER methodology and software. Based on these calculations and 2D and 3D protein descriptors, we develop statistical models for predicting the binding energy of proteins, enabling the rapid characterization of the affinity of nanoparticles to a wide range of proteins.
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19
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Abstract
Percutaneous thermal ablation has proven to be an effective modality for treating both benign and malignant tumours in various tissues. Among these modalities, radiofrequency ablation (RFA) is the most promising and widely adopted approach that has been extensively studied in the past decades. Microwave ablation (MWA) is a newly emerging modality that is gaining rapid momentum due to its capability of inducing rapid heating and attaining larger ablation volumes, and its lesser susceptibility to the heat sink effects as compared to RFA. Although the goal of both these therapies is to attain cell death in the target tissue by virtue of heating above 50°C, their underlying mechanism of action and principles greatly differs. Computational modelling is a powerful tool for studying the effect of electromagnetic interactions within the biological tissues and predicting the treatment outcomes during thermal ablative therapies. Such a priori estimation can assist the clinical practitioners during treatment planning with the goal of attaining successful tumour destruction and preservation of the surrounding healthy tissue and critical structures. This review provides current state-of-the-art developments and associated challenges in the computational modelling of thermal ablative techniques, viz., RFA and MWA, as well as touch upon several promising avenues in the modelling of laser ablation, nanoparticles assisted magnetic hyperthermia and non-invasive RFA. The application of RFA in pain relief has been extensively reviewed from modelling point of view. Additionally, future directions have also been provided to improve these models for their successful translation and integration into the hospital work flow.
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Affiliation(s)
- Sundeep Singh
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Roderick Melnik
- MS2Discovery Interdisciplinary Research Institute, Wilfrid Laurier University, Waterloo, Ontario, Canada.,BCAM - Basque Center for Applied Mathematics, Bilbao, Spain
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20
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Grebennikov DS, Donets DO, Orlova OG, Argilaguet J, Meyerhans A, Bocharov GA. [Mathematical Modeling of the Intracellular Regulation of Immune Processes]. Mol Biol (Mosk) 2019; 53:815-829. [PMID: 31661480 DOI: 10.1134/s0026898419050082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/18/2019] [Indexed: 11/23/2022]
Abstract
The modern era of research in immunology is characterized by an unprecedented level of detail about structural characteristics of the immune system and the regulation of activities of its numerous components, which function together as a whole distributed-parameter system. Mathematical modeling provides an analytical tool to describe, analyze, and predict the dynamics of immune responses by applying a reductionist approach. In modern systems immunology and mathematical immunology as a new interdisciplinary field, a great challenge is to formulate the mathematical models of the human immune system that reflect the level achieved in understanding its structure and describe the processes that sustain its function. To this end, a systematic development of multiscale mathematical models has to be advanced. An appropriate methodology should consider (1) the intracellular processes of immune cell fate regulation, (2) the population dynamics of immune cells in various organs, and (3) systemic immunophysiological processes in the whole host organism. Main studies aimed at modeling the intracellular regulatory networks are reviewed in the context of multiscale mathematical modelling. The processes considered determine the regulation of the immune cell fate, including activation, division, differentiation, apoptosis, and migration. Because of the complexity and high dimensionality of the regulatory networks, identifying the parsimonious descriptions of signaling pathways and regulatory loops is a pressing problem of modern mathematical immunology.
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Affiliation(s)
- D S Grebennikov
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, 141701 Russia.,Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences, Moscow, 119333 Russia
| | - D O Donets
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, 141701 Russia
| | - O G Orlova
- Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Moscow Region, 141701 Russia
| | - J Argilaguet
- Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, 08003 Spain
| | - A Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, 08003 Spain.,ICREA, Pg. Iluis Companys 23, Barcelona, 08010 Spain
| | - G A Bocharov
- Marchuk Institute of Numerical Mathematics, Russian Academy of Sciences, Moscow, 119333 Russia.,
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21
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Coccarelli A, Edwards DH, Aggarwal A, Nithiarasu P, Parthimos D. A multiscale active structural model of the arterial wall accounting for smooth muscle dynamics. J R Soc Interface 2019; 15:rsif.2017.0732. [PMID: 29436507 PMCID: PMC5832725 DOI: 10.1098/rsif.2017.0732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/12/2018] [Indexed: 12/13/2022] Open
Abstract
Arterial wall dynamics arise from the synergy of passive mechano-elastic properties of the vascular tissue and the active contractile behaviour of smooth muscle cells (SMCs) that form the media layer of vessels. We have developed a computational framework that incorporates both these components to account for vascular responses to mechanical and pharmacological stimuli. To validate the proposed framework and demonstrate its potential for testing hypotheses on the pathogenesis of vascular disease, we have employed a number of pharmacological probes that modulate the arterial wall contractile machinery by selectively inhibiting a range of intracellular signalling pathways. Experimental probes used on ring segments from the rabbit central ear artery are: phenylephrine, a selective α1-adrenergic receptor agonist that induces vasoconstriction; cyclopiazonic acid (CPA), a specific inhibitor of sarcoplasmic/endoplasmic reticulum Ca2+-ATPase; and ryanodine, a diterpenoid that modulates Ca2+ release from the sarcoplasmic reticulum. These interventions were able to delineate the role of membrane versus intracellular signalling, previously identified as main factors in smooth muscle contraction and the generation of vessel tone. Each SMC was modelled by a system of nonlinear differential equations that account for intracellular ionic signalling, and in particular Ca2+ dynamics. Cytosolic Ca2+ concentrations formed the catalytic input to a cross-bridge kinetics model. Contractile output from these cellular components forms the input to the finite-element model of the arterial rings under isometric conditions that reproduces the experimental conditions. The model does not account for the role of the endothelium, as the nitric oxide production was suppressed by the action of L-NAME, and also due to the absence of shear stress on the arterial ring, as the experimental set-up did not involve flow. Simulations generated by the integrated model closely matched experimental observations qualitatively, as well as quantitatively within a range of physiological parametric values. The model also illustrated how increased intercellular coupling led to smooth muscle coordination and the genesis of vascular tone.
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Affiliation(s)
- Alberto Coccarelli
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Ankush Aggarwal
- Zienkiewicz Centre for Computational Engineering, College of Engineering, Swansea University, Swansea, UK
| | - Perumal Nithiarasu
- Zienkiewicz Centre for Computational Engineering, College of Engineering, Swansea University, Swansea, UK
| | - Dimitris Parthimos
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
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22
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Friederich P, Fediai A, Kaiser S, Konrad M, Jung N, Wenzel W. Toward Design of Novel Materials for Organic Electronics. Adv Mater 2019; 31:e1808256. [PMID: 31012166 DOI: 10.1002/adma.201808256] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Indexed: 06/09/2023]
Abstract
Materials for organic electronics are presently used in prominent applications, such as displays in mobile devices, while being intensely researched for other purposes, such as organic photovoltaics, large-area devices, and thin-film transistors. Many of the challenges to improve and optimize these applications are material related and there is a nearly infinite chemical space that needs to be explored to identify the most suitable material candidates. Established experimental approaches struggle with the size and complexity of this chemical space. Herein, the development of simulation methods is addressed, with a particular emphasis on predictive multiscale protocols, to complement experimental research in the identification of novel materials and illustrate the potential of these methods with a few prominent recent applications. Finally, the potential of machine learning and methods based on artificial intelligence is discussed to further accelerate the search for new materials.
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Affiliation(s)
- Pascal Friederich
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Department of Chemistry, University of Toronto, 80 St. George Street, M5S 3H6, Toronto, Ontario, Canada
| | - Artem Fediai
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Simon Kaiser
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Manuel Konrad
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Nicole Jung
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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23
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Nikishova A, Veen L, Zun P, Hoekstra AG. Semi-intrusive multiscale metamodelling uncertainty quantification with application to a model of in-stent restenosis. Philos Trans A Math Phys Eng Sci 2019; 377:20180154. [PMID: 30967038 PMCID: PMC6388010 DOI: 10.1098/rsta.2018.0154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/10/2018] [Indexed: 05/02/2023]
Abstract
We explore the efficiency of a semi-intrusive uncertainty quantification (UQ) method for multiscale models as proposed by us in an earlier publication. We applied the multiscale metamodelling UQ method to a two-dimensional multiscale model for the wound healing response in a coronary artery after stenting (in-stent restenosis). The results obtained by the semi-intrusive method show a good match to those obtained by a black-box quasi-Monte Carlo method. Moreover, we significantly reduce the computational cost of the UQ. We conclude that the semi-intrusive metamodelling method is reliable and efficient, and can be applied to such complex models as the in-stent restenosis ISR2D model. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.
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Affiliation(s)
- A. Nikishova
- Computational Science Lab, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - L. Veen
- Netherlands eScience Center, 1098 XG Amsterdam, The Netherlands
| | - P. Zun
- Computational Science Lab, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- ITMO University, Saint Petersburg, 197101, Russia
| | - A. G. Hoekstra
- Computational Science Lab, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- ITMO University, Saint Petersburg, 197101, Russia
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24
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Abstract
For it is not the abundance of knowledge, but the interior feeling and taste of things, which is accustomed to satisfy the desire of the soul. (Saint Ignatius of Loyola). We argue that the boldest claims of big data (BD) are in need of revision and toning-down, in view of a few basic lessons learned from the science of complex systems. We point out that, once the most extravagant claims of BD are properly discarded, a synergistic merging of BD with big theory offers considerable potential to spawn a new scientific paradigm capable of overcoming some of the major barriers confronted by the modern scientific method originating with Galileo. These obstacles are due to the presence of nonlinearity, non-locality and hyperdimensions which one encounters frequently in multi-scale modelling of complex systems. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.
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Affiliation(s)
- Sauro Succi
- Center for Life Nano Sciences at La Sapienza, Istituto Italiano di Tecnologia, viale R. Margherita, 265, 00161, Roma, Italy
- Institute for Applied Computational Science, J. Paulson School of Engineering and Applied Sciences, Harvard University, 29 Oxford Street, Cambridge, USA
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London, UK
- Yale University, New Haven, USA
- e-mail:
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25
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Luk OO, Hoenen O, Perks O, Brabazon K, Piontek T, Kopta P, Bosak B, Bottino A, Scott BD, Coster DP. Application of the extreme scaling computing pattern on multiscale fusion plasma modelling. Philos Trans A Math Phys Eng Sci 2019; 377:20180152. [PMID: 30967036 PMCID: PMC6388005 DOI: 10.1098/rsta.2018.0152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/23/2018] [Indexed: 05/18/2023]
Abstract
The extreme scaling pattern of the ComPat project is applied to a multi-scale workflow relevant to the magnetically confined fusion problem. This workflow combines transport, turbulence and equilibrium codes (together with additional auxiliaries such as initial conditions and numerical module), which aims at calculating the behaviour of a fusion plasma on long (transport) time scales based on information from much faster (turbulence) time scales. Initial findings of profile measurements are reported in this paper and indicate that, depending on the chosen performance metric for defining 'cost', such as time to completion, efficiency and total energy consumption of the mutliscale workflow, different choices on the number of cores would be made when determining the optimal execution configuration. A variant of the workflow which increases the inherent parallelism is presented, and shown to produce equivalent results at (typically) lower cost compared with the original workflow. This article is part of the theme issue 'Multiscale modelling, simulation and computing: from the desktop to the exascale'.
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Affiliation(s)
- O. O. Luk
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - O. Hoenen
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | | | | | - T. Piontek
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - P. Kopta
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - B. Bosak
- Poznań Supercomputing and Networking Center, Poznań, Poland
| | - A. Bottino
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - B. D. Scott
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
| | - D. P. Coster
- Max-Planck-Institut für Plasmaphysik, Garching, Germany
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26
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Lu Y, Lee MY, Zhu S, Sinno T, Diamond SL. Multiscale simulation of thrombus growth and vessel occlusion triggered by collagen/tissue factor using a data-driven model of combinatorial platelet signalling. Math Med Biol 2018; 34:523-546. [PMID: 27672182 PMCID: PMC5798174 DOI: 10.1093/imammb/dqw015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/23/2016] [Indexed: 12/23/2022]
Abstract
During clotting under flow, platelets bind and activate on collagen and release autocrinic factors such as ADP and thromboxane, while tissue factor (TF) on the damaged wall leads to localized thrombin generation. Towards patient-specific simulation of thrombosis, a multiscale approach was developed to account for: platelet signalling [neural network (NN) trained by pairwise agonist scanning (PAS), PAS-NN], platelet positions (lattice kinetic Monte Carlo, LKMC), wall-generated thrombin and platelet-released ADP/thromboxane convection–diffusion (partial differential equation, PDE) and flow over a growing clot (lattice Boltzmann). LKMC included shear-driven platelet aggregate restructuring. The PDEs for thrombin, ADP and thromboxane were solved by finite element method using cell activation-driven adaptive triangular meshing. At all times, intracellular calcium was known for each platelet by PAS-NN in response to its unique exposure to local collagen, ADP, thromboxane and thrombin. When compared with microfluidic experiments of human blood clotting on collagen/TF driven by constant pressure drop, the model accurately predicted clot morphology and growth with time. In experiments and simulations at TF at 0.1 and 10 molecule-TF/\documentclass[12pt]{minimal}
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}{}$_{1}$\end{document} and IP-receptor. This multiscale approach facilitates patient-specific simulation of thrombosis under hemodynamic and pharmacological conditions.
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Affiliation(s)
- Yichen Lu
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Mei Yan Lee
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Shu Zhu
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
| | - Scott L Diamond
- Department of Chemical and Biomolecular Engineering, Institute for Medicine and Engineering, University of Pennsylvania, Philadelphia PA 19104, USA
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Smith CA, Yates CA. The auxiliary region method: a hybrid method for coupling PDE- and Brownian-based dynamics for reaction-diffusion systems. R Soc Open Sci 2018; 5:180920. [PMID: 30225082 PMCID: PMC6124063 DOI: 10.1098/rsos.180920] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 06/28/2018] [Indexed: 06/08/2023]
Abstract
Reaction-diffusion systems are used to represent many biological and physical phenomena. They model the random motion of particles (diffusion) and interactions between them (reactions). Such systems can be modelled at multiple scales with varying degrees of accuracy and computational efficiency. When representing genuinely multiscale phenomena, fine-scale models can be prohibitively expensive, whereas coarser models, although cheaper, often lack sufficient detail to accurately represent the phenomenon at hand. Spatial hybrid methods couple two or more of these representations in order to improve efficiency without compromising accuracy. In this paper, we present a novel spatial hybrid method, which we call the auxiliary region method (ARM), which couples PDE- and Brownian-based representations of reaction-diffusion systems. Numerical PDE solutions on one side of an interface are coupled to Brownian-based dynamics on the other side using compartment-based 'auxiliary regions'. We demonstrate that the hybrid method is able to simulate reaction-diffusion dynamics for a number of different test problems with high accuracy. Furthermore, we undertake error analysis on the ARM which demonstrates that it is robust to changes in the free parameters in the model, where previous coupling algorithms are not. In particular, we envisage that the method will be applicable for a wide range of spatial multi-scales problems including filopodial dynamics, intracellular signalling, embryogenesis and travelling wave phenomena.
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Affiliation(s)
- Cameron A. Smith
- Centre for Mathematical Biology, Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
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28
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Zarei V, Zhang S, Winkelstein BA, Barocas VH. Tissue loading and microstructure regulate the deformation of embedded nerve fibres: predictions from single-scale and multiscale simulations. J R Soc Interface 2018; 14:rsif.2017.0326. [PMID: 28978743 DOI: 10.1098/rsif.2017.0326] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/11/2017] [Indexed: 12/16/2022] Open
Abstract
Excessive deformation of nerve fibres (axons) in the spinal facet capsular ligaments (FCLs) can be a cause of pain. The axons are embedded in the fibrous extracellular matrix (ECM) of FCLs, so understanding how local fibre organization and micromechanics modulate their mechanical behaviour is essential. We constructed a computational discrete-fibre model of an axon embedded in a collagen fibre network attached to the axon by distinct fibre-axon connections. This model was used to relate the axonal deformation to the fibre alignment and collagen volume concentration of the surrounding network during transverse, axial and shear deformations. Our results showed that fibre alignment affects axonal deformation only during transverse and axial loading, but higher collagen volume concentration results in larger overall axonal strains for all loading cases. Furthermore, axial loading leads to the largest stretch of axonal microtubules and induces the largest forces on axon's surface in most cases. Comparison between this model and a multiscale continuum model for a representative case showed that although both models predicted similar averaged axonal strains, strain was more heterogeneous in the discrete-fibre model.
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Affiliation(s)
- Vahhab Zarei
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sijia Zhang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104-6321, USA
| | - Beth A Winkelstein
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104-6321, USA
| | - Victor H Barocas
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
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29
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Ouzounoglou E, Kolokotroni E, Stanulla M, Stamatakos GS. A study on the predictability of acute lymphoblastic leukaemia response to treatment using a hybrid oncosimulator. Interface Focus 2018; 8:20160163. [PMID: 29285342 PMCID: PMC5740218 DOI: 10.1098/rsfs.2016.0163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Efficient use of Virtual Physiological Human (VPH)-type models for personalized treatment response prediction purposes requires a precise model parameterization. In the case where the available personalized data are not sufficient to fully determine the parameter values, an appropriate prediction task may be followed. This study, a hybrid combination of computational optimization and machine learning methods with an already developed mechanistic model called the acute lymphoblastic leukaemia (ALL) Oncosimulator which simulates ALL progression and treatment response is presented. These methods are used in order for the parameters of the model to be estimated for retrospective cases and to be predicted for prospective ones. The parameter value prediction is based on a regression model trained on retrospective cases. The proposed Hybrid ALL Oncosimulator system has been evaluated when predicting the pre-phase treatment outcome in ALL. This has been correctly achieved for a significant percentage of patient cases tested (approx. 70% of patients). Moreover, the system is capable of denying the classification of cases for which the results are not trustworthy enough. In that case, potentially misleading predictions for a number of patients are avoided, while the classification accuracy for the remaining patient cases further increases. The results obtained are particularly encouraging regarding the soundness of the proposed methodologies and their relevance to the process of achieving clinical applicability of the proposed Hybrid ALL Oncosimulator system and VPH models in general.
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Affiliation(s)
- Eleftherios Ouzounoglou
- In Silico Oncology and In Silico Medicine Group, Institute of Communication and Computer Systems, National Technical University of Athens, Athens, Greece
| | - Eleni Kolokotroni
- In Silico Oncology and In Silico Medicine Group, Institute of Communication and Computer Systems, National Technical University of Athens, Athens, Greece
| | - Martin Stanulla
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Georgios S Stamatakos
- In Silico Oncology and In Silico Medicine Group, Institute of Communication and Computer Systems, National Technical University of Athens, Athens, Greece
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30
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Zun PS, Anikina T, Svitenkov A, Hoekstra AG. A Comparison of Fully-Coupled 3D In-Stent Restenosis Simulations to In-vivo Data. Front Physiol 2017; 8:284. [PMID: 28588498 PMCID: PMC5440556 DOI: 10.3389/fphys.2017.00284] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/19/2017] [Indexed: 01/05/2023] Open
Abstract
We describe our fully-coupled 3D multiscale model of in-stent restenosis, with blood flow simulations coupled to smooth muscle cell proliferation, and report results of numerical simulations performed with this model. This novel model is based on several previously reported 2D models. We study the effects of various parameters on the process of restenosis and compare with in vivo porcine data where we observe good qualitative agreement. We study the effects of stent deployment depth (and related injury score), reendothelization speed, and simulate the effect of stent width. Also we demonstrate that we are now capable to simulate restenosis in real-sized (18 mm long, 2.8 mm wide) vessel geometries.
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Affiliation(s)
- Pavel S. Zun
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
- Computational Science Lab, Faculty of Science, Institute for Informatics, University of AmsterdamAmsterdam, Netherlands
| | - Tatiana Anikina
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
- Computational Science Lab, Faculty of Science, Institute for Informatics, University of AmsterdamAmsterdam, Netherlands
| | - Andrew Svitenkov
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
| | - Alfons G. Hoekstra
- Saint Petersburg State University of Information Technologies, Mechanics and Optics (ITMO) UniversitySt. Petersburg, Russia
- Computational Science Lab, Faculty of Science, Institute for Informatics, University of AmsterdamAmsterdam, Netherlands
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31
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Schleicher J, Conrad T, Gustafsson M, Cedersund G, Guthke R, Linde J. Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions. Brief Funct Genomics 2017; 16:57-69. [PMID: 26857943 PMCID: PMC5439285 DOI: 10.1093/bfgp/elv064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent and rapidly evolving progress on high-throughput measurement techniques and computational performance has led to the emergence of new disciplines, such as systems medicine and translational systems biology. At the core of these disciplines lies the desire to produce multiscale models: mathematical models that integrate multiple scales of biological organization, ranging from molecular, cellular and tissue models to organ, whole-organism and population scale models. Using such models, hypotheses can systematically be tested. In this review, we present state-of-the-art multiscale modelling of bacterial and fungal infections, considering both the pathogen and host as well as their interaction. Multiscale modelling of the interactions of bacteria, especially Mycobacterium tuberculosis, with the human host is quite advanced. In contrast, models for fungal infections are still in their infancy, in particular regarding infections with the most important human pathogenic fungi, Candida albicans and Aspergillus fumigatus. We reflect on the current availability of computational approaches for multiscale modelling of host-pathogen interactions and point out current challenges. Finally, we provide an outlook for future requirements of multiscale modelling.
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Affiliation(s)
| | | | | | | | | | - Jörg Linde
- Corresponding author: Jörg Linde, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany. Tel.: +49-3641-532-1290; E-mail:
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32
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Witzke S, List NH, Olsen JMH, Steinmann C, Petersen M, Beerepoot MTP, Kongsted J. An averaged polarizable potential for multiscale modeling in phospholipid membranes. J Comput Chem 2017; 38:601-611. [PMID: 28160294 DOI: 10.1002/jcc.24718] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 01/28/2023]
Abstract
A set of average atom-centered charges and polarizabilities has been developed for three types of phospholipids for use in polarizable embedding calculations. The lipids investigated are 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, and 1-palmitoyl-2-oleoyl-sn-glycerol-3-phospho-L-serine given their common use both in experimental and computational studies. The charges, and to a lesser extent the polarizabilities, are found to depend strongly on the molecular conformation of the lipids. Furthermore, the importance of explicit polarization is underlined for the description of larger assemblies of lipids, that is, membranes. In conclusion, we find that specially developed polarizable parameters are needed for embedding calculations in membranes, while common non-polarizable point-charge force fields usually perform well enough for structural and dynamical studies. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sarah Witzke
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Nanna Holmgaard List
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | | | - Casper Steinmann
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Michael Petersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
| | - Maarten T P Beerepoot
- Centre for Theoretical and Computational Chemistry, Department of Chemistry, University of Tromsø-The Arctic University of Norway, Tromsø, N-9037, Norway
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, DK-5230, Denmark
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33
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Zhuang X, Wang Q, Zhu H. Effective Properties of Composites with Periodic Random Packing of Ellipsoids. Materials (Basel) 2017; 10:ma10020112. [PMID: 28772473 PMCID: PMC5459213 DOI: 10.3390/ma10020112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 01/03/2017] [Indexed: 11/23/2022]
Abstract
The aim of this paper is to evaluate the effective properties of composite materials with periodic random packing of ellipsoids of different volume fractions and aspect ratios. Therefore, we employ computational homogenization. A very efficient MD-based method is applied to generate the periodic random packing of the ellipsoids. The method is applicable even for extremely high volume fractions up to 60%. The influences of the volume fraction and aspect ratio on the effective properties of the composite materials are studied in several numerical examples.
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Affiliation(s)
- Xiaoying Zhuang
- Department of Geotechnical Engineering, Civil Engineering College, Tongji University, Shanghai 200092, China.
- Institute of Continuum Mechanics, Leibniz-University Hannover, 30167 Hannover, Germany.
- State Key Laboratory for Disaster Reduction in Civil Engineering, Tongji University, Shanghai 200092, China.
| | - Qing Wang
- Department of Geotechnical Engineering, Civil Engineering College, Tongji University, Shanghai 200092, China.
| | - Hehua Zhu
- Department of Geotechnical Engineering, Civil Engineering College, Tongji University, Shanghai 200092, China.
- State Key Laboratory for Disaster Reduction in Civil Engineering, Tongji University, Shanghai 200092, China.
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34
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Gooneie A, Schuschnigg S, Holzer C. A Review of Multiscale Computational Methods in Polymeric Materials. Polymers (Basel) 2017; 9:E16. [PMID: 30970697 PMCID: PMC6432151 DOI: 10.3390/polym9010016] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Polymeric materials display distinguished characteristics which stem from the interplay of phenomena at various length and time scales. Further development of polymer systems critically relies on a comprehensive understanding of the fundamentals of their hierarchical structure and behaviors. As such, the inherent multiscale nature of polymer systems is only reflected by a multiscale analysis which accounts for all important mechanisms. Since multiscale modelling is a rapidly growing multidisciplinary field, the emerging possibilities and challenges can be of a truly diverse nature. The present review attempts to provide a rather comprehensive overview of the recent developments in the field of multiscale modelling and simulation of polymeric materials. In order to understand the characteristics of the building blocks of multiscale methods, first a brief review of some significant computational methods at individual length and time scales is provided. These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). Afterwards, different prescriptions to envelope these methods in a multiscale strategy are discussed in details. Sequential, concurrent, and adaptive resolution schemes are presented along with the latest updates and ongoing challenges in research. In sequential methods, various systematic coarse-graining and backmapping approaches are addressed. For the concurrent strategy, we aimed to introduce the fundamentals and significant methods including the handshaking concept, energy-based, and force-based coupling approaches. Although such methods are very popular in metals and carbon nanomaterials, their use in polymeric materials is still limited. We have illustrated their applications in polymer science by several examples hoping for raising attention towards the existing possibilities. The relatively new adaptive resolution schemes are then covered including their advantages and shortcomings. Finally, some novel ideas in order to extend the reaches of atomistic techniques are reviewed. We conclude the review by outlining the existing challenges and possibilities for future research.
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Affiliation(s)
- Ali Gooneie
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Stephan Schuschnigg
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Clemens Holzer
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
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35
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Mannan S, Paul Knox J, Basu S. Correlations between axial stiffness and microstructure of a species of bamboo. R Soc Open Sci 2017. [PMID: 28280545 DOI: 10.5061/dryad.5ch51] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Bamboo is a ubiquitous monocotyledonous flowering plant and is a member of the true grass family Poaceae. In many parts of the world, it is widely used as a structural material especially in scaffolding and buildings. In spite of its wide use, there is no accepted methodology for standardizing a species of bamboo for a particular structural purpose. The task of developing structure-property correlations is complicated by the fact that bamboo is a hierarchical material whose structure at the nanoscopic level is not very well explored. However, we show that as far as stiffness is concerned, it is possible to obtain reliable estimates of important structural properties like the axial modulus from the knowledge of certain key elements of the microstructure. Stiffness of bamboo depends most sensitively on the size and arrangement of the fibre sheaths surrounding the vascular bundles and the arrangement of crystalline cellulose microfibrils in their secondary cell walls. For the species of bamboo studied in this work, we have quantitatively determined the radial gradation that the arrangement of fibres renders to the structure. The arrangement of the fibres gives bamboo a radially graded property variation across its cross section.
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Affiliation(s)
- Sayyad Mannan
- Department of Mechanical Engineering , Indian Institute of Technology Kanpur , Kanpur , Uttar Pradesh 208016 , India
| | - J Paul Knox
- Centre for Plant Sciences , Faculty of Biological Sciences , University of Leeds , Leeds LS2 9JT , UK
| | - Sumit Basu
- Department of Mechanical Engineering , Indian Institute of Technology Kanpur , Kanpur , Uttar Pradesh 208016 , India
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36
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Mannan S, Paul Knox J, Basu S. Correlations between axial stiffness and microstructure of a species of bamboo. R Soc Open Sci 2017; 4:160412. [PMID: 28280545 PMCID: PMC5319311 DOI: 10.1098/rsos.160412] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/14/2016] [Indexed: 06/06/2023]
Abstract
Bamboo is a ubiquitous monocotyledonous flowering plant and is a member of the true grass family Poaceae. In many parts of the world, it is widely used as a structural material especially in scaffolding and buildings. In spite of its wide use, there is no accepted methodology for standardizing a species of bamboo for a particular structural purpose. The task of developing structure-property correlations is complicated by the fact that bamboo is a hierarchical material whose structure at the nanoscopic level is not very well explored. However, we show that as far as stiffness is concerned, it is possible to obtain reliable estimates of important structural properties like the axial modulus from the knowledge of certain key elements of the microstructure. Stiffness of bamboo depends most sensitively on the size and arrangement of the fibre sheaths surrounding the vascular bundles and the arrangement of crystalline cellulose microfibrils in their secondary cell walls. For the species of bamboo studied in this work, we have quantitatively determined the radial gradation that the arrangement of fibres renders to the structure. The arrangement of the fibres gives bamboo a radially graded property variation across its cross section.
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Affiliation(s)
- Sayyad Mannan
- Department of Mechanical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - J. Paul Knox
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Sumit Basu
- Department of Mechanical Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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37
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Levrero-Florencio F, Manda K, Margetts L, Pankaj P. Nonlinear homogenisation of trabecular bone: Effect of solid phase constitutive model. Proc Inst Mech Eng H 2016; 231:405-414. [PMID: 28427317 DOI: 10.1177/0954411916676220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Micro-finite element models have been extensively employed to evaluate the elastic properties of trabecular bone and, to a limited extent, its yield behaviour. The macroscopic stiffness tensor and yield surface are of special interest since they are essential in the prediction of bone strength and stability of implants at the whole bone level. While macroscopic elastic properties are now well understood, yield and post-yield properties are not. The aim of this study is to shed some light on what the effect of the solid phase yield criterion is on the macroscopic yield of trabecular bone for samples with different microstructure. Three samples with very different density were subjected to a large set of apparent load cases (which is important since physiological loading is complex and can have multiple components in stress or strain space) with two different solid phase yield criteria: Drucker-Prager and eccentric-ellipsoid. The study found that these two criteria led to small differences in the macroscopic yield strains for most load cases except for those that were compression-dominated; in these load cases, the yield strains for the Drucker-Prager criterion were significantly higher. Higher density samples resulted in higher differences between the two criteria. This work provides a comprehensive assessment of the effect of two different solid phase yield criteria on the macroscopic yield strains of trabecular bone, for a wide range of load cases, and for samples with different morphology.
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Affiliation(s)
| | - Krishnagoud Manda
- 1 Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, UK
| | - Lee Margetts
- 2 School of Mechanical, Aerospace and Civil Engineering The University of Manchester Sackville Street Manchester, UK
| | - Pankaj Pankaj
- 1 Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, UK
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Schmitz GJ, Böttger B, Apel M, Eiken J, Laschet G, Altenfeld R, Berger R, Boussinot G, Viardin A. Towards a metadata scheme for the description of materials - the description of microstructures. Sci Technol Adv Mater 2016; 17:410-430. [PMID: 27877892 PMCID: PMC5111567 DOI: 10.1080/14686996.2016.1194166] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 05/12/2016] [Accepted: 05/23/2016] [Indexed: 06/01/2023]
Abstract
The property of any material is essentially determined by its microstructure. Numerical models are increasingly the focus of modern engineering as helpful tools for tailoring and optimization of custom-designed microstructures by suitable processing and alloy design. A huge variety of software tools is available to predict various microstructural aspects for different materials. In the general frame of an integrated computational materials engineering (ICME) approach, these microstructure models provide the link between models operating at the atomistic or electronic scales, and models operating on the macroscopic scale of the component and its processing. In view of an improved interoperability of all these different tools it is highly desirable to establish a standardized nomenclature and methodology for the exchange of microstructure data. The scope of this article is to provide a comprehensive system of metadata descriptors for the description of a 3D microstructure. The presented descriptors are limited to a mere geometric description of a static microstructure and have to be complemented by further descriptors, e.g. for properties, numerical representations, kinetic data, and others in the future. Further attributes to each descriptor, e.g. on data origin, data uncertainty, and data validity range are being defined in ongoing work. The proposed descriptors are intended to be independent of any specific numerical representation. The descriptors defined in this article may serve as a first basis for standardization and will simplify the data exchange between different numerical models, as well as promote the integration of experimental data into numerical models of microstructures. An HDF5 template data file for a simple, three phase Al-Cu microstructure being based on the defined descriptors complements this article.
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Affiliation(s)
| | | | - Markus Apel
- MICRESS® group at Access e.V., Aachen, Germany
| | - Janin Eiken
- MICRESS® group at Access e.V., Aachen, Germany
| | | | | | - Ralf Berger
- MICRESS® group at Access e.V., Aachen, Germany
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Kurzeja P. The criterion of subscale sufficiency and its application to the relationship between static capillary pressure, saturation and interfacial areas. Proc Math Phys Eng Sci 2016; 472:20150869. [PMID: 27279769 DOI: 10.1098/rspa.2015.0869] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Modern imaging techniques, increased simulation capabilities and extended theoretical frameworks, naturally drive the development of multiscale modelling by the question: which new information should be considered? Given the need for concise constitutive relationships and efficient data evaluation; however, one important question is often neglected: which information is sufficient? For this reason, this work introduces the formalized criterion of subscale sufficiency. This criterion states whether a chosen constitutive relationship transfers all necessary information from micro to macroscale within a multiscale framework. It further provides a scheme to improve constitutive relationships. Direct application to static capillary pressure demonstrates usefulness and conditions for subscale sufficiency of saturation and interfacial areas.
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Affiliation(s)
- Patrick Kurzeja
- Institute of Mechanics-Continuum Mechanics, Ruhr-University Bochum, 44780 Bochum, Germany; John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Faculty of Physics, University of Duisburg-Essen, 47048 Duisburg, Germany
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40
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Wimmer Y, El-Sayed AM, Gös W, Grasser T, Shluger AL. Role of hydrogen in volatile behaviour of defects in SiO 2-based electronic devices. Proc Math Phys Eng Sci 2016; 472:20160009. [PMID: 27436969 PMCID: PMC4950194 DOI: 10.1098/rspa.2016.0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 05/31/2016] [Indexed: 11/12/2022] Open
Abstract
Charge capture and emission by point defects in gate oxides of metal-oxide-semiconductor field-effect transistors (MOSFETs) strongly affect reliability and performance of electronic devices. Recent advances in experimental techniques used for probing defect properties have led to new insights into their characteristics. In particular, these experimental data show a repeated dis- and reappearance (the so-called volatility) of the defect-related signals. We use multiscale modelling to explain the charge capture and emission as well as defect volatility in amorphous SiO2 gate dielectrics. We first briefly discuss the recent experimental results and use a multiphonon charge capture model to describe the charge-trapping behaviour of defects in silicon-based MOSFETs. We then link this model to ab initio calculations that investigate the three most promising defect candidates. Statistical distributions of defect characteristics obtained from ab initio calculations in amorphous SiO2 are compared with the experimentally measured statistical properties of charge traps. This allows us to suggest an atomistic mechanism to explain the experimentally observed volatile behaviour of defects. We conclude that the hydroxyl-E' centre is a promising candidate to explain all the observed features, including defect volatility.
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Affiliation(s)
- Yannick Wimmer
- Institute for Microelectronics, Vienna University of Technology, Gußhausstraße 27–29/E360, 1040 Wien, Austria
| | - Al-Moatasem El-Sayed
- Institute for Microelectronics, Vienna University of Technology, Gußhausstraße 27–29/E360, 1040 Wien, Austria
- Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, UK
| | - Wolfgang Gös
- Institute for Microelectronics, Vienna University of Technology, Gußhausstraße 27–29/E360, 1040 Wien, Austria
| | - Tibor Grasser
- Institute for Microelectronics, Vienna University of Technology, Gußhausstraße 27–29/E360, 1040 Wien, Austria
| | - Alexander L. Shluger
- Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT, UK
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41
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Fernandez J, Zhang J, Heidlauf T, Sartori M, Besier T, Röhrle O, Lloyd D. Multiscale musculoskeletal modelling, data-model fusion and electromyography-informed modelling. Interface Focus 2016; 6:20150084. [PMID: 27051510 DOI: 10.1098/rsfs.2015.0084] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This paper proposes methods and technologies that advance the state of the art for modelling the musculoskeletal system across the spatial and temporal scales; and storing these using efficient ontologies and tools. We present population-based modelling as an efficient method to rapidly generate individual morphology from only a few measurements and to learn from the ever-increasing supply of imaging data available. We present multiscale methods for continuum muscle and bone models; and efficient mechanostatistical methods, both continuum and particle-based, to bridge the scales. Finally, we examine both the importance that muscles play in bone remodelling stimuli and the latest muscle force prediction methods that use electromyography-assisted modelling techniques to compute musculoskeletal forces that best reflect the underlying neuromuscular activity. Our proposal is that, in order to have a clinically relevant virtual physiological human, (i) bone and muscle mechanics must be considered together; (ii) models should be trained on population data to permit rapid generation and use underlying principal modes that describe both muscle patterns and morphology; and (iii) these tools need to be available in an open-source repository so that the scientific community may use, personalize and contribute to the database of models.
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Affiliation(s)
- J Fernandez
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - J Zhang
- Auckland Bioengineering Institute , University of Auckland , Auckland , New Zealand
| | - T Heidlauf
- Institut für Mechanik (Bau) , University of Stuttgart , Stuttgart , Germany
| | - M Sartori
- Department of Neurorehabilitation Engineering , University Medical Center Göttingen , Göttingen , Germany
| | - T Besier
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand; Department of Engineering Science, University of Auckland, Auckland, New Zealand
| | - O Röhrle
- Institut für Mechanik (Bau) , University of Stuttgart , Stuttgart , Germany
| | - D Lloyd
- Centre for Musculoskeletal Research, Menzies Health Institute Queensland, Griffith University, Queensland, Australia; School of Rehabilitation Sciences, Griffith University, Queensland, Australia
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42
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Li Y, Lian Y, Zhang LT, Aldousari SM, Hedia HS, Asiri SA, Liu WK. Cell and nanoparticle transport in tumour microvasculature: the role of size, shape and surface functionality of nanoparticles. Interface Focus 2016; 6:20150086. [PMID: 26855759 DOI: 10.1098/rsfs.2015.0086] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Through nanomedicine, game-changing methods are emerging to deliver drug molecules directly to diseased areas. One of the most promising of these is the targeted delivery of drugs and imaging agents via drug carrier-based platforms. Such drug delivery systems can now be synthesized from a wide range of different materials, made in a number of different shapes, and coated with an array of different organic molecules, including ligands. If optimized, these systems can enhance the efficacy and specificity of delivery compared with those of non-targeted systems. Emerging integrated multiscale experiments, models and simulations have opened the door for endless medical applications. Current bottlenecks in design of the drug-carrying particles are the lack of knowledge about the dispersion of these particles in the microvasculature and of their subsequent internalization by diseased cells (Bao et al. 2014 J. R. Soc. Interface 11, 20140301 (doi:10.1098/rsif.2014.0301)). We describe multiscale modelling techniques that study how drug carriers disperse within the microvasculature. The immersed molecular finite-element method is adopted to simulate whole blood including blood plasma, red blood cells and nanoparticles. With a novel dissipative particle dynamics method, the beginning stages of receptor-driven endocytosis of nanoparticles can be understood in detail. Using this multiscale modelling method, we elucidate how the size, shape and surface functionality of nanoparticles will affect their dispersion in the microvasculature and subsequent internalization by targeted cells.
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Affiliation(s)
- Ying Li
- Department of Mechanical Engineering and Institute of Materials Science , University of Connecticut , Storrs, CT 06269 , USA
| | - Yanping Lian
- Department of Mechanical Engineering , Northwestern University , Evanston, IL 60201 , USA
| | - Lucy T Zhang
- Department of Mechanical, Aerospace and Nuclear Engineering , Rensselaer Polytechnic Institute , Troy, NY 12189 , USA
| | - Saad M Aldousari
- Department of Mechanical Engineering , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Hassan S Hedia
- Department of Mechanical Engineering , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Saeed A Asiri
- Department of Mechanical Engineering , King Abdulaziz University , Jeddah , Saudi Arabia
| | - Wing Kam Liu
- Department of Mechanical Engineering, Northwestern University, Evanston, IL 60201, USA; Distinguished Scientists Program Committee, King Abdulaziz University, Jeddah, Saudi Arabia
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43
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Smith LJ, Deymier AC, Boyle JJ, Li Z, Linderman SW, Pasteris JD, Xia Y, Genin GM, Thomopoulos S. Tunability of collagen matrix mechanical properties via multiple modes of mineralization. Interface Focus 2016; 6:20150070. [PMID: 26855755 DOI: 10.1098/rsfs.2015.0070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Functionally graded, mineralized collagen tissues exist at soft-to-hard material attachments throughout the body. However, the details of how collagen and hydroxyapatite mineral (HA) interact are not fully understood, hampering efforts to develop tissue-engineered constructs that can assist with repair of injuries at the attachments of soft tissues to bone. In this study, spatial control of mineralization was achieved in collagen matrices using simulated body fluids (SBFs). Based upon previous observations of poor bonding between reconstituted collagen and HA deposited using SBF, we hypothesized that mineralizing collagen in the presence of fetuin (which inhibits surface mineralization) would lead to more mineral deposition within the scaffold and therefore a greater increase in stiffness and toughness compared with collagen mineralized without fetuin. We tested this hypothesis through integrated synthesis, mechanical testing and modelling of graded, mineralized reconstituted collagen constructs. Results supported the hypothesis, and further suggested that mineralization on the interior of reconstituted collagen constructs, as promoted by fetuin, led to superior bonding between HA and collagen. The results provide us guidance for the development of mineralized collagen scaffolds, with implications for bone and tendon-to-bone tissue engineering.
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Affiliation(s)
- Lester J Smith
- Department of Orthopaedic Surgery , Washington University , St Louis, MO 63130 , USA
| | - Alix C Deymier
- Department of Orthopaedic Surgery , Washington University , St Louis, MO 63130 , USA
| | - John J Boyle
- Department of Orthopaedic Surgery, Washington University, St Louis, MO 63130, USA; Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
| | - Zhen Li
- Department of Earth and Planetary Sciences , Washington University , St Louis, MO 63130 , USA
| | - Stephen W Linderman
- Department of Orthopaedic Surgery, Washington University, St Louis, MO 63130, USA; Department of Biomedical Engineering, Washington University, St Louis, MO 63130, USA
| | - Jill D Pasteris
- Department of Earth and Planetary Sciences , Washington University , St Louis, MO 63130 , USA
| | - Younan Xia
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Guy M Genin
- Department of Mechanical Engineering and Materials Science , Washington University , St Louis, MO 63130 , USA
| | - Stavros Thomopoulos
- Department of Orthopedic Surgery, Columbia University, New York, NY 10032, USA; Department of Biomedical Engineering, Columbia University, New York, NY 10032, USA
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Abstract
In this paper, we review analytical and computational models of bone fracture and strength. Bone fracture is a complex phenomenon due to the composite, inhomogeneous and hierarchical structure of bone. First, we briefly summarize the hierarchical structure of bone, spanning from the nanoscale, sub-microscale, microscale, mesoscale to the macroscale, and discuss experimental observations on failure mechanisms in bone at these scales. Then, we highlight representative analytical and computational models of bone fracture and strength at different length scales and discuss the main findings in the context of experiments. We conclude by summarizing the challenges in modelling of bone fracture and strength and list open topics for scientific exploration. Modelling of bone, accounting for different scales, provides new and needed insights into the fracture and strength of bone, which, in turn, can lead to improved diagnostic tools and treatments of bone diseases such as osteoporosis.
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Affiliation(s)
| | | | | | - Iwona Jasiuk
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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45
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Abstract
Advances in multiscale models and computational power have enabled a broad toolset to predict how molecules, cells, tissues and organs behave and develop. A key theme in biological systems is the emergence of macroscale behaviour from collective behaviours across a range of length and timescales, and a key element of these models is therefore hierarchical simulation. However, this predictive capacity has far outstripped our ability to validate predictions experimentally, particularly when multiple hierarchical levels are involved. The state of the art represents careful integration of multiscale experiment and modelling, and yields not only validation, but also insights into deformation and relaxation mechanisms across scales. We present here a sampling of key results that highlight both challenges and opportunities for integrated multiscale experiment and modelling in biological systems.
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Affiliation(s)
- Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Guy M Genin
- Department of Mechanical Engineering and Materials Science, and Department of Neurological Surgery, Washington University, St Louis, MO 63130, USA
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46
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Erban R. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics. Proc Math Phys Eng Sci 2016; 472:20150556. [PMID: 27118886 PMCID: PMC4841651 DOI: 10.1098/rspa.2015.0556] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022] Open
Abstract
Molecular dynamics (MD) simulations of ions (K+, Na+, Ca2+ and Cl-) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parametrized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.
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Affiliation(s)
- Radek Erban
- Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford OX2 6GG, UK
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47
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Yates CA, Flegg MB. The pseudo-compartment method for coupling partial differential equation and compartment-based models of diffusion. J R Soc Interface 2015; 12:20150141. [PMID: 25904527 PMCID: PMC4424691 DOI: 10.1098/rsif.2015.0141] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/30/2015] [Indexed: 12/27/2022] Open
Abstract
Spatial reaction-diffusion models have been employed to describe many emergent phenomena in biological systems. The modelling technique most commonly adopted in the literature implements systems of partial differential equations (PDEs), which assumes there are sufficient densities of particles that a continuum approximation is valid. However, owing to recent advances in computational power, the simulation and therefore postulation, of computationally intensive individual-based models has become a popular way to investigate the effects of noise in reaction-diffusion systems in which regions of low copy numbers exist. The specific stochastic models with which we shall be concerned in this manuscript are referred to as 'compartment-based' or 'on-lattice'. These models are characterized by a discretization of the computational domain into a grid/lattice of 'compartments'. Within each compartment, particles are assumed to be well mixed and are permitted to react with other particles within their compartment or to transfer between neighbouring compartments. Stochastic models provide accuracy, but at the cost of significant computational resources. For models that have regions of both low and high concentrations, it is often desirable, for reasons of efficiency, to employ coupled multi-scale modelling paradigms. In this work, we develop two hybrid algorithms in which a PDE in one region of the domain is coupled to a compartment-based model in the other. Rather than attempting to balance average fluxes, our algorithms answer a more fundamental question: 'how are individual particles transported between the vastly different model descriptions?' First, we present an algorithm derived by carefully redefining the continuous PDE concentration as a probability distribution. While this first algorithm shows very strong convergence to analytical solutions of test problems, it can be cumbersome to simulate. Our second algorithm is a simplified and more efficient implementation of the first, it is derived in the continuum limit over the PDE region alone. We test our hybrid methods for functionality and accuracy in a variety of different scenarios by comparing the averaged simulations with analytical solutions of PDEs for mean concentrations.
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Affiliation(s)
- Christian A Yates
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Mark B Flegg
- School of Mathematical Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia
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Abstract
One of the greatest challenges in biomedicine is to get a unified view of observations made from the molecular up to the organism scale. Towards this goal, multiscale models have been highly instrumental in contexts such as the cardiovascular field, angiogenesis, neurosciences and tumour biology. More recently, such models are becoming an increasingly important resource to address immunological questions as well. Systematic mining of the literature in multiscale modelling led us to identify three main fields of immunological applications: host-virus interactions, inflammatory diseases and their treatment and development of multiscale simulation platforms for immunological research and for educational purposes. Here, we review the current developments in these directions, which illustrate that multiscale models can consistently integrate immunological data generated at several scales, and can be used to describe and optimize therapeutic treatments of complex immune diseases.
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Affiliation(s)
- Antonio Cappuccio
- Laboratory of Integrative biology of human dendritic cells and T cells, U932 Immunity and cancer, Institut Curie, 26 Rue d`Ulm, 75005 Paris, France
| | - Paolo Tieri
- Institute for Applied Mathematics (IAC), National Research Council of Italy (CNR), Via dei Taurini 19, 00185 Rome, Italy
| | - Filippo Castiglione
- Institute for Applied Mathematics (IAC), National Research Council of Italy (CNR), Via dei Taurini 19, 00185 Rome, Italy
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Markesteijn A, Karabasov S, Scukins A, Nerukh D, Glotov V, Goloviznin V. Concurrent multiscale modelling of atomistic and hydrodynamic processes in liquids. Philos Trans A Math Phys Eng Sci 2014; 372:rsta.2013.0379. [PMID: 24982246 PMCID: PMC4084524 DOI: 10.1098/rsta.2013.0379] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Fluctuations of liquids at the scales where the hydrodynamic and atomistic descriptions overlap are considered. The importance of these fluctuations for atomistic motions is discussed and examples of their accurate modelling with a multi-space-time-scale fluctuating hydrodynamics scheme are provided. To resolve microscopic details of liquid systems, including biomolecular solutions, together with macroscopic fluctuations in space-time, a novel hybrid atomistic-fluctuating hydrodynamics approach is introduced. For a smooth transition between the atomistic and continuum representations, an analogy with two-phase hydrodynamics is used that leads to a strict preservation of macroscopic mass and momentum conservation laws. Examples of numerical implementation of the new hybrid approach for the multiscale simulation of liquid argon in equilibrium conditions are provided.
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Affiliation(s)
- Anton Markesteijn
- Department of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Sergey Karabasov
- Department of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Arturs Scukins
- Department of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Dmitry Nerukh
- Department of Engineering and Applied Science, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Vyacheslav Glotov
- Department of Mathematical Modelling, Moscow Institute of Nuclear Safety, 113191 Moscow, Russia
| | - Vasily Goloviznin
- Department of Mathematical Modelling, Moscow Institute of Nuclear Safety, 113191 Moscow, Russia
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50
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Voß U, Bishopp A, Farcot E, Bennett MJ. Modelling hormonal response and development. Trends Plant Sci 2014; 19:311-9. [PMID: 24630843 PMCID: PMC4013931 DOI: 10.1016/j.tplants.2014.02.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 02/05/2014] [Accepted: 02/07/2014] [Indexed: 05/20/2023]
Abstract
As our knowledge of the complexity of hormone homeostasis, transport, perception, and response increases, and their outputs become less intuitive, modelling is set to become more important. Initial modelling efforts have focused on hormone transport and response pathways. However, we now need to move beyond the network scales and use multicellular and multiscale modelling approaches to predict emergent properties at different scales. Here we review some examples where such approaches have been successful, for example, auxin-cytokinin crosstalk regulating root vascular development or a study of lateral root emergence where an iterative cycle of modelling and experiments lead to the identification of an overlooked role for PIN3. Finally, we discuss some of the remaining biological and technical challenges.
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Affiliation(s)
- Ute Voß
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK
| | - Etienne Farcot
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK; School of Mathematical Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Malcolm J Bennett
- Centre for Plant Integrative Biology, University of Nottingham, Nottingham, LE12 5RD, UK.
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