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Colizzi ES, Hogeweg P, Vroomans RMA. Modelling the evolution of novelty: a review. Essays Biochem 2022; 66:727-735. [PMID: 36468669 PMCID: PMC9750852 DOI: 10.1042/ebc20220069] [Citation(s) in RCA: 1] [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] [Received: 09/12/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022]
Abstract
Evolution has been an inventive process since its inception, about 4 billion years ago. It has generated an astounding diversity of novel mechanisms and structures for adaptation to the environment, for competition and cooperation, and for organisation of the internal and external dynamics of the organism. How does this novelty come about? Evolution builds with the tools available, and on top of what it has already built - therefore, much novelty consists in repurposing old functions in a different context. In the process, the tools themselves evolve, allowing yet more novelty to arise. Despite evolutionary novelty being the most striking observable of evolution, it is not accounted for in classical evolutionary theory. Nevertheless, mathematical and computational models that illustrate mechanisms of evolutionary innovation have been developed. In the present review, we present and compare several examples of computational evo-devo models that capture two aspects of novelty: 'between-level novelty' and 'constructive novelty.' Novelty can evolve between predefined levels of organisation to dynamically transcode biological information across these levels - as occurs during development. Constructive novelty instead generates a level of biological organisation by exploiting the lower level as an informational scaffold to open a new space of possibilities - an example being the evolution of multicellularity. We propose that the field of computational evo-devo is well-poised to reveal many more exciting mechanisms for the evolution of novelty. A broader theory of evolutionary novelty may well be attainable in the near future.
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Affiliation(s)
- Enrico Sandro Colizzi
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, CB2 1LR, Cambridge, U.K
| | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics, Universiteit Utrecht, Padualaan 8, 3584 CH, Utrecht, Netherlands
| | - Renske M A Vroomans
- Sainsbury Laboratory, University of Cambridge, 47 Bateman Street, CB2 1LR, Cambridge, U.K
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2
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Waites W, Cavaliere M, Danos V, Datta R, Eggo RM, Hallett TB, Manheim D, Panovska-Griffiths J, Russell TW, Zarnitsyna VI. Compositional modelling of immune response and virus transmission dynamics. Philos Trans A Math Phys Eng Sci 2022; 380:20210307. [PMID: 35965463 PMCID: PMC9376723 DOI: 10.1098/rsta.2021.0307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 05/02/2023]
Abstract
Transmission models for infectious diseases are typically formulated in terms of dynamics between individuals or groups with processes such as disease progression or recovery for each individual captured phenomenologically, without reference to underlying biological processes. Furthermore, the construction of these models is often monolithic: they do not allow one to readily modify the processes involved or include the new ones, or to combine models at different scales. We show how to construct a simple model of immune response to a respiratory virus and a model of transmission using an easily modifiable set of rules allowing further refining and merging the two models together. The immune response model reproduces the expected response curve of PCR testing for COVID-19 and implies a long-tailed distribution of infectiousness reflective of individual heterogeneity. This immune response model, when combined with a transmission model, reproduces the previously reported shift in the population distribution of viral loads along an epidemic trajectory. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.
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Affiliation(s)
- W. Waites
- Department of Computer and Information Sciences, University of Strathclyde, Glasgow, UK
- Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene and Tropical Medicine, London, UK
| | - M. Cavaliere
- Department of Computing and Mathematics, Manchester Metropolitan University, Manchester, UK
| | - V. Danos
- Département d’Informatique, École Normale Supérieure, Paris, France
| | - R. Datta
- Datta Enterprises LLC, San Francisco, CA, USA
| | - R. M. Eggo
- Department of Computer and Information Sciences, University of Strathclyde, Glasgow, UK
| | - T. B. Hallett
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK
| | - D. Manheim
- Technion, Israel Institute of Technology, Haifa, Israel
| | - J. Panovska-Griffiths
- The Big Data Institute and the Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Queen’s College, University of Oxford, Oxford, UK
| | - T. W. Russell
- Department of Computer and Information Sciences, University of Strathclyde, Glasgow, UK
| | - V. I. Zarnitsyna
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
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3
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Barberis M, Rojas López A. T cell phenotype switching in autoimmune disorders: Clinical significance of targeting metabolism. Clin Transl Med 2022; 12:e898. [PMID: 35904141 PMCID: PMC9335893 DOI: 10.1002/ctm2.898] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 05/10/2022] [Indexed: 12/31/2022] Open
Abstract
Increasing efforts points to the understanding of how to maximize the capabilities of the adaptive immune system to fight against the development of immune and inflammatory disorders. Here we focus on the role of T cells as immune cells which subtype imbalance may lead to disease onset. Specifically, we propose that autoimmune disorders may develop as a consequence of a metabolic imbalance that modulates switching between T cell phenotypes. We highlight a Systems Biology strategy that integrates computational metabolic modelling with experimental data to investigate the metabolic requirements of T cell phenotypes, and to predict metabolic genes that may be targeted in autoimmune inflammatory diseases. Thus, we propose a new perspective of targeting T cell metabolism to modulate the immune response and prevent T cell phenotype imbalance, which may help to repurpose already existing drugs targeting metabolism for therapeutic treatment.
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Affiliation(s)
- Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, UK.,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Alejandra Rojas López
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, UK
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4
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Saikia E, Läubli NF, Burri JT, Rüggeberg M, Vogler H, Burgert I, Herrmann HJ, Nelson BJ, Grossniklaus U, Wittel FK. Kinematics Governing Mechanotransduction in the Sensory Hair of the Venus flytrap. Int J Mol Sci 2020; 22:E280. [PMID: 33396579 DOI: 10.3390/ijms22010280] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Insects fall prey to the Venus flytrap (Dionaea muscipula) when they touch the sensory hairs located on the flytrap lobes, causing sudden trap closure. The mechanical stimulus imparted by the touch produces an electrical response in the sensory cells of the trigger hair. These cells are found in a constriction near the hair base, where a notch appears around the hair’s periphery. There are mechanosensitive ion channels (MSCs) in the sensory cells that open due to a change in membrane tension; however, the kinematics behind this process is unclear. In this study, we investigate how the stimulus acts on the sensory cells by building a multi-scale hair model, using morphometric data obtained from μ-CT scans. We simulated a single-touch stimulus and evaluated the resulting cell wall stretch. Interestingly, the model showed that high stretch values are diverted away from the notch periphery and, instead, localized in the interior regions of the cell wall. We repeated our simulations for different cell shape variants to elucidate how the morphology influences the location of these high-stretch regions. Our results suggest that there is likely a higher mechanotransduction activity in these ’hotspots’, which may provide new insights into the arrangement and functioning of MSCs in the flytrap. Dataset: 10.3929/ethz-b-000448954
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Sinchuk Y, Kibleur P, Aelterman J, Boone MN, Van Paepegem W. Variational and Deep Learning Segmentation of Very-low-contrast X-ray Computed Tomography Images of Carbon/Epoxy Woven Composites. Materials (Basel) 2020; 13:ma13040936. [PMID: 32093177 PMCID: PMC7079634 DOI: 10.3390/ma13040936] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/15/2020] [Accepted: 02/17/2020] [Indexed: 11/16/2022]
Abstract
The purpose of this work is to find an effective image segmentation method for lab-based micro-tomography (µ-CT) data of carbon fiber reinforced polymers (CFRP) with insufficient contrast-to-noise ratio. The segmentation is the first step in creating a realistic geometry (based on µ-CT) for finite element modelling of textile composites on meso-scale. Noise in X-ray imaging data of carbon/polymer composites forms a challenge for this segmentation due to the very low X-ray contrast between fiber and polymer and unclear fiber gradients. To the best of our knowledge, segmentation of µ-CT images of carbon/polymer textile composites with low resolution data (voxel size close to the fiber diameter) remains poorly documented. In this paper, we propose and evaluate different approaches for solving the segmentation problem: variational on the one hand and deep-learning-based on the other. In the author’s view, both strategies present a novel and reliable ground for the segmentation of µ-CT data of CFRP woven composites. The predictions of both approaches were evaluated against a manual segmentation of the volume, constituting our “ground truth”, which provides quantitative data on the segmentation accuracy. The highest segmentation accuracy (about 4.7% in terms of voxel-wise Dice similarity) was achieved using the deep learning approach with U-Net neural network.
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Affiliation(s)
- Yuriy Sinchuk
- Department of Materials Science and Engineering, Faculty of Engineering and Architecture, Ghent University, Technologiepark Zwijnaarde 46, 9052 Zwijnaarde, Belgium;
- Correspondence:
| | - Pierre Kibleur
- Department of Environment, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Gent, Belgium;
- Center for X-ray Tomography (UGCT), Ghent University, Proeftuinstraat 86, 9000 Gent, Belgium; (J.A.); (M.N.B.)
| | - Jan Aelterman
- Center for X-ray Tomography (UGCT), Ghent University, Proeftuinstraat 86, 9000 Gent, Belgium; (J.A.); (M.N.B.)
- Department of Telecommunications and Information Processing–Image Processing and Interpretation, Faculty of Engineering and Architecture, Ghent University—IMEC, Sint-Pietersnieuwstraat 41, 9000 Gent, Belgium
- Department of Physics and Astronomy, Faculty of Sciences, Ghent University, Proeftuinstraat 86, 9000 Gent, Belgium
| | - Matthieu N. Boone
- Center for X-ray Tomography (UGCT), Ghent University, Proeftuinstraat 86, 9000 Gent, Belgium; (J.A.); (M.N.B.)
- Department of Physics and Astronomy, Faculty of Sciences, Ghent University, Proeftuinstraat 86, 9000 Gent, Belgium
| | - Wim Van Paepegem
- Department of Materials Science and Engineering, Faculty of Engineering and Architecture, Ghent University, Technologiepark Zwijnaarde 46, 9052 Zwijnaarde, Belgium;
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Galenko PK, Alexandrov DV. From atomistic interfaces to dendritic patterns. Philos Trans A Math Phys Eng Sci 2018; 376:rsta.2017.0210. [PMID: 29311208 PMCID: PMC5784100 DOI: 10.1098/rsta.2017.0210] [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] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/01/2017] [Indexed: 05/24/2023]
Abstract
Transport processes around phase interfaces, together with thermodynamic properties and kinetic phenomena, control the formation of dendritic patterns. Using the thermodynamic and kinetic data of phase interfaces obtained on the atomic scale, one can analyse the formation of a single dendrite and the growth of a dendritic ensemble. This is the result of recent progress in theoretical methods and computational algorithms calculated using powerful computer clusters. Great benefits can be attained from the development of micro-, meso- and macro-levels of analysis when investigating the dynamics of interfaces, interpreting experimental data and designing the macrostructure of samples. The review and research articles in this theme issue cover the spectrum of scales (from nano- to macro-length scales) in order to exhibit recently developing trends in the theoretical analysis and computational modelling of dendrite pattern formation. Atomistic modelling, the flow effect on interface dynamics, the transition from diffusion-limited to thermally controlled growth existing at a considerable driving force, two-phase (mushy) layer formation, the growth of eutectic dendrites, the formation of a secondary dendritic network due to coalescence, computational methods, including boundary integral and phase-field methods, and experimental tests for theoretical models-all these themes are highlighted in the present issue.This article is part of the theme issue 'From atomistic interfaces to dendritic patterns'.
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Affiliation(s)
- P K Galenko
- Physikalisch-Astronomische Fakultät, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - D V Alexandrov
- Department of Theoretical and Mathematical Physics, Laboratory of Multi-Scale Mathematical Modeling, Ural Federal University, Ekaterinburg 620000, Russian Federation
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Beaumont PWR, Soutis C. Structural integrity of engineering composite materials: a cracking good yarn. Philos Trans A Math Phys Eng Sci 2016; 374:20160057. [PMID: 27242293 PMCID: PMC4901257 DOI: 10.1098/rsta.2016.0057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
Predicting precisely where a crack will develop in a material under stress and exactly when in time catastrophic fracture of the component will occur is one the oldest unsolved mysteries in the design and building of large-scale engineering structures. Where human life depends upon engineering ingenuity, the burden of testing to prove a 'fracture safe design' is immense. Fitness considerations for long-life implementation of large composite structures include understanding phenomena such as impact, fatigue, creep and stress corrosion cracking that affect reliability, life expectancy and durability of structure. Structural integrity analysis treats the design, the materials used, and figures out how best components and parts can be joined, and takes service duty into account. However, there are conflicting aims in the complete design process of designing simultaneously for high efficiency and safety assurance throughout an economically viable lifetime with an acceptable level of risk. This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'.
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Affiliation(s)
| | - Costas Soutis
- Aerospace Research Institute, NW Composites Centre and NCCEF, University of Manchester, Manchester, UK
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8
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Saucedo-Mora L, Marrow TJ. Multi-scale damage modelling in a ceramic matrix composite using a finite-element microstructure meshfree methodology. Philos Trans A Math Phys Eng Sci 2016; 374:20150276. [PMID: 27242308 PMCID: PMC4901247 DOI: 10.1098/rsta.2015.0276] [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] [Subscribe] [Scholar Register] [Accepted: 03/18/2016] [Indexed: 06/05/2023]
Abstract
The problem of multi-scale modelling of damage development in a SiC ceramic fibre-reinforced SiC matrix ceramic composite tube is addressed, with the objective of demonstrating the ability of the finite-element microstructure meshfree (FEMME) model to introduce important aspects of the microstructure into a larger scale model of the component. These are particularly the location, orientation and geometry of significant porosity and the load-carrying capability and quasi-brittle failure behaviour of the fibre tows. The FEMME model uses finite-element and cellular automata layers, connected by a meshfree layer, to efficiently couple the damage in the microstructure with the strain field at the component level. Comparison is made with experimental observations of damage development in an axially loaded composite tube, studied by X-ray computed tomography and digital volume correlation. Recommendations are made for further development of the model to achieve greater fidelity to the microstructure. This article is part of the themed issue 'Multiscale modelling of the structural integrity of composite materials'.
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Affiliation(s)
- L Saucedo-Mora
- Institute Eduardo Torroja for Construction Sciences-CSIC, Madrid, Spain
| | - T J Marrow
- Department of Materials, University of Oxford, Oxford, UK
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9
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Madeo A, Barbagallo G, d’Agostino MV, Placidi L, Neff P. First evidence of non-locality in real band-gap metamaterials: determining parameters in the relaxed micromorphic model. Proc Math Phys Eng Sci 2016; 472:20160169. [PMID: 27436984 PMCID: PMC4949383 DOI: 10.1098/rspa.2016.0169] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 05/06/2016] [Indexed: 11/12/2022] Open
Abstract
In this paper, we propose the first estimate of some elastic parameters of the relaxed micromorphic model on the basis of real experiments of transmission of longitudinal plane waves across an interface separating a classical Cauchy material (steel plate) and a phononic crystal (steel plate with fluid-filled holes). A procedure is set up in order to identify the parameters of the relaxed micromorphic model by superimposing the experimentally based profile of the reflection coefficient (plotted as function of the wave-frequency) with the analogous profile obtained via numerical simulations. We determine five out of six constitutive parameters which are featured by the relaxed micromorphic model in the isotropic case, plus the determination of the micro-inertia parameter. The sixth elastic parameter, namely the Cosserat couple modulus μc , still remains undetermined, since experiments on transverse incident waves are not yet available. A fundamental result of this paper is the estimate of the non-locality intrinsically associated with the underlying microstructure of the metamaterial. We show that the characteristic length Lc measuring the non-locality of the phononic crystal is of the order of [Formula: see text] of the diameter of its fluid-filled holes.
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Affiliation(s)
- Angela Madeo
- LGCIE, Universitité de Lyon, 20 av. Albert Einstein, 69621, Villeurbanne cedex, France
| | - Gabriele Barbagallo
- LGCIE, Universitité de Lyon, 20 av. Albert Einstein, 69621, Villeurbanne cedex, France
- LaMCoS-CNRS, INSA-Lyon, Universitité de Lyon, 20 av. Albert Einstein, 69621, Villeurbanne cedex, France
| | | | - Luca Placidi
- Università Telematica Internazionale UNINETTUNO, Corso Vittorio Emanuele II, 39, 00186 Roma, Italy
| | - Patrizio Neff
- Fakultät für Mathematik, Universität Duisburg-Essen, Thea-Leymann-Straße 9, 45127 Essen, Germany
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Pant S, Fabrèges B, Gerbeau JF, Vignon-Clementel IE. A methodological paradigm for patient-specific multi-scale CFD simulations: from clinical measurements to parameter estimates for individual analysis. Int J Numer Method Biomed Eng 2014; 30:1614-1648. [PMID: 25345820 DOI: 10.1002/cnm.2692] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [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: 06/18/2014] [Revised: 09/19/2014] [Accepted: 10/19/2014] [Indexed: 06/04/2023]
Abstract
A new framework for estimation of lumped (for instance, Windkessel) model parameters from uncertain clinical measurements is presented. The ultimate aim is to perform patient-specific haemodynamic analysis. This framework is based on sensitivity analysis tools and the sequential estimation approach of the unscented Kalman filter. Sensitivity analysis and parameter estimation are performed in lumped parameter models, which act as reduced order surrogates of the 3D domain for haemodynamic analysis. While the goal of sensitivity analysis is to assess potential identifiability problems, the unscented Kalman filter estimation leads to parameter estimates based on clinical measurements and modelling assumptions. An application of such analysis and parameter estimation methodology is demonstrated for synthetic and real data. Equality constraints on various physiological parameters are enforced. Since the accuracy of the Windkessel parameter estimates depends on the lumped parameter representativeness, the latter is iteratively improved by running few 3D simulations while simultaneously improving the former. Such a method is applied on a patient-specific aortic coarctation case. Less than 3% and 9% errors between the clinically measured quantities and 3D simulation results for rest and stress are obtained, respectively. Knowledge on how these Windkessel parameters change from rest to stress can thus be learned by such an approach. Lastly, it is demonstrated that the proposed approach is capable of dealing with a wide variety of measurements and cases where the pressure and flow clinical measurements are not taken simultaneously.
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Affiliation(s)
- S Pant
- INRIA Paris-Rocquencourt, 78153 Le Chesnay, France; UPMC Université Paris 6, Laboratoire Jacques-Louis Lions, 75005 Paris, France
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Abstract
Active soft matter is a young, growing field, with potential applications to a wide variety of systems. This Theme Issue explores this emerging new field by highlighting active liquid crystals. The collected contributions bridge theory to experiment, mathematical theories of passive and active nematics, spontaneous flows to defect dynamics, microscopic to continuum levels of description, spontaneous activity to biological activation. While the perspectives offered here only span a small part of this rapidly evolving field, we trust that they might provide the interested reader with a taste for this new class of non-equilibrium systems and their rich behaviour.
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Affiliation(s)
- Apala Majumdar
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Marchetti M Cristina
- Department of Physics, and Syracuse Biomaterials Institute, Syracuse University, Syracuse, NY 13244, USA
| | - Epifanio G Virga
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, Pavia 27100, Italy
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12
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Li X, Peng Z, Lei H, Dao M, Karniadakis GE. Probing red blood cell mechanics, rheology and dynamics with a two-component multi-scale model. Philos Trans A Math Phys Eng Sci 2014; 372:20130389. [PMID: 24982252 PMCID: PMC4084529 DOI: 10.1098/rsta.2013.0389] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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] [Indexed: 05/29/2023]
Abstract
This study is partially motivated by the validation of a new two-component multi-scale cell model we developed recently that treats the lipid bilayer and the cytoskeleton as two distinct components. Here, the whole cell model is validated and compared against several available experiments that examine red blood cell (RBC) mechanics, rheology and dynamics. First, we investigated RBC deformability in a microfluidic channel with a very small cross-sectional area and quantified the mechanical properties of the RBC membrane. Second, we simulated twisting torque cytometry and compared predicted rheological properties of the RBC membrane with experimental measurements. Finally, we modelled the tank-treading (TT) motion of a RBC in a shear flow and explored the effect of channel width variation on the TT frequency. We also investigated the effects of bilayer-cytoskeletal interactions on these experiments and our simulations clearly indicated that they play key roles in the determination of cell membrane mechanical, rheological and dynamical properties. These simulations serve as validation tests and moreover reveal the capabilities and limitations of the new whole cell model.
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Affiliation(s)
- Xuejin Li
- Division of Applied Mathematics, Brown University, Providence, RI 02912, USA
| | - Zhangli Peng
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Huan Lei
- Computational Sciences and Mathematics Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Ming Dao
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Abstract
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analysing multi-scale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD) simulations in the remainder of the domain. The first MD model is formulated in one spatial dimension. It is based on elastic collisions of heavy molecules (e.g. proteins) with light point particles (e.g. water molecules). Two three-dimensional MD models are then investigated. The obtained results are applied to a simplified model of protein binding to receptors on the cellular membrane. It is shown that modern BD simulators of intracellular processes can be used in the bulk and accurately coupled with a (more detailed) MD model of protein binding which is used close to the membrane.
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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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Logsdon EA, Finley SD, Popel AS, Mac Gabhann F. A systems biology view of blood vessel growth and remodelling. J Cell Mol Med 2013; 18:1491-508. [PMID: 24237862 PMCID: PMC4190897 DOI: 10.1111/jcmm.12164] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022] Open
Abstract
Blood travels throughout the body in an extensive network of vessels – arteries, veins and capillaries. This vascular network is not static, but instead dynamically remodels in response to stimuli from cells in the nearby tissue. In particular, the smallest vessels – arterioles, venules and capillaries – can be extended, expanded or pruned, in response to exercise, ischaemic events, pharmacological interventions, or other physiological and pathophysiological events. In this review, we describe the multi-step morphogenic process of angiogenesis – the sprouting of new blood vessels – and the stability of vascular networks in vivo. In particular, we review the known interactions between endothelial cells and the various blood cells and plasma components they convey. We describe progress that has been made in applying computational modelling, quantitative biology and high-throughput experimentation to the angiogenesis process.
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Affiliation(s)
- Elizabeth A Logsdon
- Institute for Computational Medicine and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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15
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Domínguez-Hüttinger E, Ono M, Barahona M, Tanaka RJ. Risk factor-dependent dynamics of atopic dermatitis: modelling multi-scale regulation of epithelium homeostasis. Interface Focus 2013; 3:20120090. [PMID: 23853706 PMCID: PMC3638487 DOI: 10.1098/rsfs.2012.0090] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Epithelial tissue provides the body with its first layer of protection against harmful environmental stimuli by enacting the regulatory interplay between a physical barrier preventing the influx of external stimuli and an inflammatory response to the infiltrating stimuli. Importantly, this interdependent regulation occurs on different time scales: the tissue-level barrier permeability is regulated over the course of hours, whereas the cellular-level enzymatic reactions leading to inflammation take place within minutes. This multi-scale regulation is key to the epithelium's function and its dysfunction leads to various diseases. This paper presents a mathematical model of regulatory mechanisms in the epidermal epithelium that includes processes on two different time scales at the cellular and tissue levels. We use this model to investigate the essential regulatory interactions between epidermal barrier integrity and skin inflammation and how their dysfunction leads to atopic dermatitis (AD). Our model exhibits a structure of dual (positive and negative) control at both cellular and tissue levels. We also determined how the variation induced by well-known risk factors for AD can break the balance of the dual control. Our model analysis based on time-scale separation suggests that each risk factor leads to qualitatively different dynamic behaviours of different severity for AD, and that the coincidence of multiple risk factors dramatically increases the fragility of the epithelium's function. The proposed mathematical framework should also be applicable to other inflammatory diseases that have similar time-scale separation and control architectures.
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16
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Wolkenhauer O, Green S. The search for organizing principles as a cure against reductionism in systems medicine. FEBS J 2013; 280:5938-48. [PMID: 23621685 DOI: 10.1111/febs.12311] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [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: 01/31/2013] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 12/23/2022]
Abstract
Biological complexity has forced scientists to develop highly reductive approaches, with an ever-increasing degree of specialization. As a consequence, research projects have become fragmented, and their results strongly dependent on the experimental context. The general research question, that originally motivated these projects, appears to have been forgotten in many highly specialized research programmes. We here investigate the prospects for use of an old regulative ideal from systems theory to describe the organization of cellular systems 'in general' by identifying key concepts, challenges and strategies to pursue the search for organizing principles. We argue that there is no tension between the complexity of biological systems and the search for organizing principles. On the contrary, it is the complexity of organisms and the current level of techniques and knowledge that urge us to renew the search for organizing principles in order to meet the challenges that are arise from reductive approaches in systems medicine. Reductive approaches, as important and inevitable as they are, should be complemented by an integrative strategy that de-contextualizes through abstractions, and thereby generalizes results.
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Affiliation(s)
- Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, Germany; Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, South Africa
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Bernabeu MO, Nash RW, Groen D, Carver HB, Hetherington J, Krüger T, Coveney PV. Impact of blood rheology on wall shear stress in a model of the middle cerebral artery. Interface Focus 2013; 3:20120094. [PMID: 24427534 PMCID: PMC3638489 DOI: 10.1098/rsfs.2012.0094] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Perturbations to the homeostatic distribution of mechanical forces exerted by blood on the endothelial layer have been correlated with vascular pathologies, including intracranial aneurysms and atherosclerosis. Recent computational work suggests that, in order to correctly characterize such forces, the shear-thinning properties of blood must be taken into account. To the best of our knowledge, these findings have never been compared against experimentally observed pathological thresholds. In this work, we apply the three-band diagram (TBD) analysis due to Gizzi et al. (Gizzi et al. 2011 Three-band decomposition analysis of wall shear stress in pulsatile flows. Phys. Rev. E 83, 031902. (doi:10.1103/PhysRevE.83.031902)) to assess the impact of the choice of blood rheology model on a computational model of the right middle cerebral artery. Our results show that, in the model under study, the differences between the wall shear stress predicted by a Newtonian model and the well-known Carreau-Yasuda generalized Newtonian model are only significant if the vascular pathology under study is associated with a pathological threshold in the range 0.94-1.56 Pa, where the results of the TBD analysis of the rheology models considered differs. Otherwise, we observe no significant differences.
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Affiliation(s)
- Miguel O. Bernabeu
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
- CoMPLEX, University College London, Physics Building, Gower Street, London WC1E 6BT, UK
| | - Rupert W. Nash
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Derek Groen
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Hywel B. Carver
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
- CoMPLEX, University College London, Physics Building, Gower Street, London WC1E 6BT, UK
| | - James Hetherington
- Research Software Development Team, Research Computing and Facilitating Services, University College London, Podium Building, 1st Floor, Gower Street, London WC1E 6BT, UK
| | - Timm Krüger
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, UK
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Hosseini SA, Shah N. Multi-scale process and supply chain modelling: from lignocellulosic feedstock to process and products. Interface Focus 2011; 1:255-62. [PMID: 22482032 DOI: 10.1098/rsfs.2010.0013] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/11/2011] [Indexed: 11/12/2022] Open
Abstract
There is a large body of literature regarding the choice and optimization of different processes for converting feedstock to bioethanol and bio-commodities; moreover, there has been some reasonable technological development in bioconversion methods over the past decade. However, the eventual cost and other important metrics relating to sustainability of biofuel production will be determined not only by the performance of the conversion process, but also by the performance of the entire supply chain from feedstock production to consumption. Moreover, in order to ensure world-class biorefinery performance, both the network and the individual components must be designed appropriately, and allocation of resources over the resulting infrastructure must effectively be performed. The goal of this work is to describe the key challenges in bioenergy supply chain modelling and then to develop a framework and methodology to show how multi-scale modelling can pave the way to answer holistic supply chain questions, such as the prospects for second generation bioenergy crops.
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Affiliation(s)
- Seyed Ali Hosseini
- Department of Chemical Engineering, Faculty of Engineering and Physical Sciences , University of Surrey , Guildford GU2 7XH , UK
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Tahir H, Hoekstra AG, Lorenz E, Lawford PV, Hose DR, Gunn J, Evans DJW. Multi-scale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design. Interface Focus 2011; 1:365-73. [PMID: 22670206 DOI: 10.1098/rsfs.2010.0024] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [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: 11/15/2010] [Accepted: 03/03/2011] [Indexed: 12/11/2022] Open
Abstract
Neointimal hyperplasia, a process of smooth muscle cell re-growth, is the result of a natural wound healing response of the injured artery after stent deployment. Excessive neointimal hyperplasia following coronary artery stenting results in in-stent restenosis (ISR). Regardless of recent developments in the field of coronary stent design, ISR remains a significant complication of this interventional therapy. The influence of stent design parameters such as strut thickness, shape and the depth of strut deployment within the vessel wall on the severity of restenosis has already been highlighted but the detail of this influence is unclear. These factors impact on local haemodynamics and vessel structure and affect the rate of neointima formation. This paper presents the first results of a multi-scale model of ISR. The development of the simulated restenosis as a function of stent deployment depth is compared with an in vivo porcine dataset. Moreover, the influence of strut size and shape is investigated, and the effect of a drug released at the site of injury, by means of a drug-eluting stent, is also examined. A strong correlation between strut thickness and the rate of smooth muscle cell proliferation has been observed. Simulation results also suggest that the growth of the restenotic lesion is strongly dependent on the stent strut cross-sectional profile.
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Affiliation(s)
- Hannan Tahir
- Computational Science, Faculty of Science , University of Amsterdam , Amsterdam , The Netherlands
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Hunter P, Coveney PV, de Bono B, Diaz V, Fenner J, Frangi AF, Harris P, Hose R, Kohl P, Lawford P, McCormack K, Mendes M, Omholt S, Quarteroni A, Skår J, Tegner J, Randall Thomas S, Tollis I, Tsamardinos I, van Beek JHGM, Viceconti M. A vision and strategy for the virtual physiological human in 2010 and beyond. Philos Trans A Math Phys Eng Sci 2010; 368:2595-614. [PMID: 20439264 PMCID: PMC2944384 DOI: 10.1098/rsta.2010.0048] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [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] [Indexed: 05/29/2023]
Abstract
European funding under framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for nearly 2 years. The VPH network of excellence (NoE) is helping in the development of common standards, open-source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also helping to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by framework 6 strategy for a European physiome (STEP) project in 2006. It is now time to assess the accomplishments of the last 2 years and update the STEP vision for the VPH. We consider the biomedical science, healthcare and information and communications technology challenges facing the project and we propose the VPH Institute as a means of sustaining the vision of VPH beyond the time frame of the NoE.
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Affiliation(s)
- Peter Hunter
- Auckland Bioengineering Institute (ABI ), University of Auckland, , Auckland, New Zealand.
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21
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Xu F, Moon S, Zhang X, Shao L, Song YS, Demirci U. Multi-scale heat and mass transfer modelling of cell and tissue cryopreservation. Philos Trans A Math Phys Eng Sci 2010; 368:561-83. [PMID: 20047939 PMCID: PMC3263795 DOI: 10.1098/rsta.2009.0248] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [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] [Indexed: 05/04/2023]
Abstract
Cells and tissues undergo complex physical processes during cryopreservation. Understanding the underlying physical phenomena is critical to improve current cryopreservation methods and to develop new techniques. Here, we describe multi-scale approaches for modelling cell and tissue cryopreservation including heat transfer at macroscale level, crystallization, cell volume change and mass transport across cell membranes at microscale level. These multi-scale approaches allow us to study cell and tissue cryopreservation.
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Affiliation(s)
- Feng Xu
- Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Bioengineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sangjun Moon
- Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Bioengineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaohui Zhang
- Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Bioengineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lei Shao
- Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Bioengineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Young Seok Song
- Polymer System Division, Fiber System Engineering, Dankook University, Yongin-si, Gyeonggi-do, Korea
- Author for correspondence (; )
| | - Utkan Demirci
- Bio-Acoustic-MEMS in Medicine (BAMM) Laboratory, Center for Bioengineering, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Harvard-Massachusetts Institute of Technology Health Sciences and Technology, Cambridge, MA, USA
- Author for correspondence (; )
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Díaz-Zuccarini V, Narracott AJ, Burriesci G, Zervides C, Rafiroiu D, Jones D, Hose DR, Lawford PV. Adaptation and development of software simulation methodologies for cardiovascular engineering: present and future challenges from an end-user perspective. Philos Trans A Math Phys Eng Sci 2009; 367:2655-2666. [PMID: 19487202 PMCID: PMC2696108 DOI: 10.1098/rsta.2009.0052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This paper describes the use of diverse software tools in cardiovascular applications. These tools were primarily developed in the field of engineering and the applications presented push the boundaries of the software to address events related to venous and arterial valve closure, exploration of dynamic boundary conditions or the inclusion of multi-scale boundary conditions from protein to organ levels. The future of cardiovascular research and the challenges that modellers and clinicians face from validation to clinical uptake are discussed from an end-user perspective.
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Affiliation(s)
- V Díaz-Zuccarini
- Cardiovascular Engineering and Medical Devices Group, Department of Mechanical Engineering, University College London, Torrington Place, London WC1 7JE, UK.
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23
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Plank G, Burton RAB, Hales P, Bishop M, Mansoori T, Bernabeu MO, Garny A, Prassl AJ, Bollensdorff C, Mason F, Mahmood F, Rodriguez B, Grau V, Schneider JE, Gavaghan D, Kohl P. Generation of histo-anatomically representative models of the individual heart: tools and application. Philos Trans A Math Phys Eng Sci 2009; 367:2257-92. [PMID: 19414455 PMCID: PMC2881535 DOI: 10.1098/rsta.2009.0056] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [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] [Indexed: 05/22/2023]
Abstract
This paper presents methods to build histo-anatomically detailed individualized cardiac models. The models are based on high-resolution three-dimensional anatomical and/or diffusion tensor magnetic resonance images, combined with serial histological sectioning data, and are used to investigate individualized cardiac function. The current state of the art is reviewed, and its limitations are discussed. We assess the challenges associated with the generation of histo-anatomically representative individualized in silico models of the heart. The entire processing pipeline including image acquisition, image processing, mesh generation, model set-up and execution of computer simulations, and the underlying methods are described. The multifaceted challenges associated with these goals are highlighted, suitable solutions are proposed, and an important application of developed high-resolution structure-function models in elucidating the effect of individual structural heterogeneity upon wavefront dynamics is demonstrated.
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Affiliation(s)
- Gernot Plank
- Computational Biology Group, University of Oxford, Oxford OX1 2JD, UK.
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