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Walker BJ, Townsend AK, Chudasama AK, Krause AL. VisualPDE: Rapid Interactive Simulations of Partial Differential Equations. Bull Math Biol 2023; 85:113. [PMID: 37823924 PMCID: PMC10570185 DOI: 10.1007/s11538-023-01218-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Computing has revolutionised the study of complex nonlinear systems, both by allowing us to solve previously intractable models and through the ability to visualise solutions in different ways. Using ubiquitous computing infrastructure, we provide a means to go one step further in using computers to understand complex models through instantaneous and interactive exploration. This ubiquitous infrastructure has enormous potential in education, outreach and research. Here, we present VisualPDE, an online, interactive solver for a broad class of 1D and 2D partial differential equation (PDE) systems. Abstract dynamical systems concepts such as symmetry-breaking instabilities, subcritical bifurcations and the role of initial data in multistable nonlinear models become much more intuitive when you can play with these models yourself, and immediately answer questions about how the system responds to changes in parameters, initial conditions, boundary conditions or even spatiotemporal forcing. Importantly, VisualPDE is freely available, open source and highly customisable. We give several examples in teaching, research and knowledge exchange, providing high-level discussions of how it may be employed in different settings. This includes designing web-based course materials structured around interactive simulations, or easily crafting specific simulations that can be shared with students or collaborators via a simple URL. We envisage VisualPDE becoming an invaluable resource for teaching and research in mathematical biology and beyond. We also hope that it inspires other efforts to make mathematics more interactive and accessible.
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Affiliation(s)
- Benjamin J Walker
- Department of Mathematical Sciences, University of Bath, Bath, BA2 7AY, UK
- Department of Mathematics, University College London, London, WC1E 6BT, UK
| | - Adam K Townsend
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, UK
| | - Alexander K Chudasama
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, UK
| | - Andrew L Krause
- Department of Mathematical Sciences, Durham University, Upper Mountjoy Campus, Stockton Road, Durham, DH1 3LE, UK.
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Greene D, Kaboudian A, Wasserstrom JA, Fenton FH, Shiferaw Y. Voltage-mediated mechanism for calcium wave synchronization and arrhythmogenesis in atrial tissue. Biophys J 2022; 121:383-395. [PMID: 34968425 PMCID: PMC8822619 DOI: 10.1016/j.bpj.2021.12.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
A wide range of atrial arrythmias are caused by molecular defects in proteins that regulate calcium (Ca) cycling. In many cases, these defects promote the propagation of subcellular Ca waves in the cell, which can perturb the voltage time course and induce dangerous perturbations of the action potential (AP). However, subcellular Ca waves occur randomly in cells and, therefore, electrical coupling between cells substantially decreases their effect on the AP. In this study, we present evidence that Ca waves in atrial tissue can synchronize in-phase owing to an order-disorder phase transition. In particular, we show that, below a critical pacing rate, Ca waves are desynchronized and therefore do not induce substantial AP fluctuations in tissue. However, above this critical pacing rate, Ca waves gradually synchronize over millions of cells, which leads to a dramatic amplification of AP fluctuations. We exploit an underlying Ising symmetry of paced cardiac tissue to show that this transition exhibits universal properties common to a wide range of physical systems in nature. Finally, we show that in the heart, phase synchronization induces spatially out-of-phase AP duration alternans which drives wave break and reentry. These results suggest that cardiac tissue exhibits a phase transition that is required for subcellular Ca cycling defects to induce a life-threatening arrhythmia.
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Affiliation(s)
- D'Artagnan Greene
- Department of Physics and Astronomy, California State University, Northridge, California
| | - Abouzar Kaboudian
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - John A Wasserstrom
- The Feinberg Cardiovascular and Renal Research Institute, Department of Medicine (Cardiology), Northwestern University, Feinberg School of Medicine, Chicago, Illinois
| | - Flavio H Fenton
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Yohannes Shiferaw
- Department of Physics and Astronomy, California State University, Northridge, California.
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Berman JP, Kaboudian A, Uzelac I, Iravanian S, Iles T, Iaizzo PA, Lim H, Smolka S, Glimm J, Cherry EM, Fenton FH. Interactive 3D Human Heart Simulations on Segmented Human MRI Hearts. COMPUTING IN CARDIOLOGY 2021; 48:10.23919/cinc53138.2021.9662948. [PMID: 35754523 PMCID: PMC9228622 DOI: 10.23919/cinc53138.2021.9662948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Understanding cardiac arrhythmic mechanisms and developing new strategies to control and terminate them using computer simulations requires realistic physiological cell models with anatomically accurate heart structures. Furthermore, numerical simulations must be fast enough to study and validate model and structure parameters. Here, we present an interactive parallel approach for solving detailed cell dynamics in high-resolution human heart structures with a local PC's GPU. In vitro human heart MRI scans were manually segmented to produce 3D structures with anatomically realistic electrophysiology. The Abubu.js library was used to create an interactive code to solve the OVVR human ventricular cell model and the FDA extension of the model in the human MRI heart structures, allowing the simulation of reentrant waves and investigation of their dynamics in real time. Interactive simulations of a physiological cell model in a detailed anatomical human heart reveals propagation of waves through the fine structures of the trabeculae and pectinate muscle that can perpetuate arrhythmias, thereby giving new insights into effects that may need to be considered when planning ablation and other defibrillation methods.
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Affiliation(s)
- John P Berman
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Abouzar Kaboudian
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Ilija Uzelac
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Tinen Iles
- Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Paul A Iaizzo
- Medical School, University of Minnesota, Minneapolis, MN, USA
| | | | | | | | - Elizabeth M Cherry
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Flavio H Fenton
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
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Kaboudian A, Cherry EM, Fenton FH. Real-Time Interactive Simulations of Complex Ionic Cardiac Cell Models in 2D and 3D Heart Structures with GPUs on Personal Computers. COMPUTING IN CARDIOLOGY 2021; 48:10.23919/cinc53138.2021.9662759. [PMID: 35754517 PMCID: PMC9228612 DOI: 10.23919/cinc53138.2021.9662759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
AIMS Cardiac modeling in heart structures for the study of arrhythmia mechanisms requires the use of software that runs on supercomputers. Therefore, computational studies are limited to groups with access to computer clusters and personnel with high-performance computing experience. We present how to use and implement WebGL programs via a custom-written library to run and visualize simulations of the most complex ionic models in 2D and 3D, in real time, interactively using the multi-core GPU of a single computer. METHODS We use Abubu.js, a library we developed for solving partial differential equations such as those describing crystal growth and fluid flow, along with a newly implemented visualization algorithm, to simulate complex ionic cell models. By combining this library with JavaScript, we allow direct real-time interactions with simulations. We implemented: 1) modification of any model parameters and equations at any time, with direct access to the code while it runs, 2) electrode stimulation anywhere in the 2D/3D tissue with a mouse click, 3) saving the solution of the system at any time to re-initiate the dynamics from saved initial conditions, and 4) rotation/visualization of 3D structures at any angle. RESULTS As examples of this modeling platform, we implemented a phenomenological cell model and the human ventricular OVVR model (41 variables). In 2D we illustrate the dynamics in an annulus, disk, and square tissue; in 2D and 3D porcine ventricles, we show the initiation of functional/anatomical reentry, spiral wave dynamics in different regimes, initiation of early afterdepolarizations (EADs), and the effects of model parameter variations in real time. CONCLUSIONS We present the first simulations of complex models in anatomical structures with enhanced visualization and extended interactivity that run on a single PC, without software downloads, and as fast as in real-time even for 3D full ventricles.
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Affiliation(s)
- Abouzar Kaboudian
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Elizabeth M Cherry
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Flavio H Fenton
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
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Pathmanathan P, Galappaththige SK, Cordeiro JM, Kaboudian A, Fenton FH, Gray RA. Data-Driven Uncertainty Quantification for Cardiac Electrophysiological Models: Impact of Physiological Variability on Action Potential and Spiral Wave Dynamics. Front Physiol 2020; 11:585400. [PMID: 33329034 PMCID: PMC7711195 DOI: 10.3389/fphys.2020.585400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022] Open
Abstract
Computational modeling of cardiac electrophysiology (EP) has recently transitioned from a scientific research tool to clinical applications. To ensure reliability of clinical or regulatory decisions made using cardiac EP models, it is vital to evaluate the uncertainty in model predictions. Model predictions are uncertain because there is typically substantial uncertainty in model input parameters, due to measurement error or natural variability. While there has been much recent uncertainty quantification (UQ) research for cardiac EP models, all previous work has been limited by either: (i) considering uncertainty in only a subset of the full set of parameters; and/or (ii) assigning arbitrary variation to parameters (e.g., ±10 or 50% around mean value) rather than basing the parameter uncertainty on experimental data. In our recent work we overcame the first limitation by performing UQ and sensitivity analysis using a novel canine action potential model, allowing all parameters to be uncertain, but with arbitrary variation. Here, we address the second limitation by extending our previous work to use data-driven estimates of parameter uncertainty. Overall, we estimated uncertainty due to population variability in all parameters in five currents active during repolarization: inward potassium rectifier, transient outward potassium, L-type calcium, rapidly and slowly activating delayed potassium rectifier; 25 parameters in total (all model parameters except fast sodium current parameters). A variety of methods was used to estimate the variability in these parameters. We then propagated the uncertainties through the model to determine their impact on predictions of action potential shape, action potential duration (APD) prolongation due to drug block, and spiral wave dynamics. Parameter uncertainty had a significant effect on model predictions, especially L-type calcium current parameters. Correlation between physiological parameters was determined to play a role in physiological realism of action potentials. Surprisingly, even model outputs that were relative differences, specifically drug-induced APD prolongation, were heavily impacted by the underlying uncertainty. This is the first data-driven end-to-end UQ analysis in cardiac EP accounting for uncertainty in the vast majority of parameters, including first in tissue, and demonstrates how future UQ could be used to ensure model-based decisions are robust to all underlying parameter uncertainties.
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Affiliation(s)
- Pras Pathmanathan
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, MD, United States
| | - Suran K. Galappaththige
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, MD, United States
| | - Jonathan M. Cordeiro
- Department of Experimental Cardiology, Masonic Medical Research Institute, Utica, NY, United States
| | - Abouzar Kaboudian
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Flavio H. Fenton
- School of Physics, Georgia Institute of Technology, Atlanta, GA, United States
| | - Richard A. Gray
- U.S. Food and Drug Administration, Center for Devices and Radiological Health, Silver Spring, MD, United States
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Abstract
Modern scientific visualization is web-based and uses emerging technology such as WebGL (Web Graphics Library) and WebGPU for three-dimensional computer graphics and WebXR for augmented and virtual reality devices. These technologies, paired with the accessibility of websites, potentially offer a user experience beyond traditional standalone visualization systems. We review the state-of-the-art of web-based scientific visualization and present an overview of existing methods categorized by application domain. As part of this analysis, we introduce the Scientific Visualization Future Readiness Score (SciVis FRS) to rank visualizations for a technology-driven disruptive tomorrow. We then summarize challenges, current state of the publication trend, future directions, and opportunities for this exciting research field.
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Welsh AJ, Delgado C, Lee-Trimble C, Kaboudian A, Fenton FH. Simulating waves, chaos and synchronization with a microcontroller. CHAOS (WOODBURY, N.Y.) 2019; 29:123104. [PMID: 31893636 PMCID: PMC7195869 DOI: 10.1063/1.5094351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 10/22/2019] [Indexed: 05/12/2023]
Abstract
The spatiotemporal dynamics of complex systems have been studied traditionally and visualized numerically using high-end computers. However, due to advances in microcontrollers, it is now possible to run what once were considered large-scale simulations using a very small and inexpensive single integrated circuit that can furthermore send and receive information to and from the outside world in real time. In this paper, we show how microcontrollers can be used to perform simulations of nonlinear ordinary differential equations with spatial coupling and to visualize their dynamics using arrays of light-emitting diodes and/or touchscreens. We demonstrate these abilities using three different models: two reaction-diffusion models (one neural and one cardiac) and a generic model of network oscillators. These models are commonly used to simulate various phenomena in biophysical systems, including bifurcations, waves, chaos, and synchronization. We also demonstrate how simple it is to integrate real-time user interaction with the simulations by showing examples with a light sensor, touchscreen, and web browser.
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Affiliation(s)
- Andrea J Welsh
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Cristian Delgado
- Facultad de Ciencias, Universidad Nacional Autònoma de México, Distrito Federal 04510, Mexico
| | | | - Abouzar Kaboudian
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Flavio H Fenton
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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