Research Collaboration Visit to the Auckland Bioengineering Institute, New Zealand.

Lead Research Organisation: University of Liverpool
Department Name: Computer Science

Abstract

Despite over a century's study, the mechanisms of cardiac arrhythmias are poorly understood. Even modern experimental methods do not provide sufficient temporal and spacial resolution to trace down fine details of fibrillation development in samples of cardiac tissue, not to mention the heart in vivo. Advances in human genetics provide information on the impact of certain genes on cellular activity, but do not explain the resultant mechanisms by which fibrillation arises. Thus, for some genetic cardiac diseases, the first presenting symptom is death.

Combination of mathematical modelling and the latest realistic computer simulations of electrical activity in the heart have much advanced our understanding of heart fibrillation and sudden cardiac death, and the impact of in-silico modelling, or indeed in-silico "testing", is expected to increase significantly as we approach the ultimate goal of the whole-heart modelling.

Biophysically and anatomically realistic simulation of cardiac action potential propagation through the heart is computationally expensive due to the huge number of equations per cell and the vast spacial and temporal scales required. Therefore any insights that can be obtained through generic mathematical model analysis is very valuable, as it tends to reveal generic mechanisms, unlike direct computer simulations, which provide answers valid only for a specific choice of parameters and initial conditions and depend on the computer model accuracy. Note that despite of the decades of steady progress, computer models still have qualitative rather than quantitative predictive power on the macroscopic scale, e.g. where whole heart or a whole chamber of the heart are concerned.

Our recent progress in asymptotic analysis of dissipative vortices dynamics has revealed a new phenomenon of the vortices interaction with sharp variations of thickness in excitable layer. Such interaction of cardiac re-entry with sharp anatomical features, as e.g. pectinate muscles and terminal crest in atria, can cause considerable displacement of established localisation of re-entry compared to where it was first localised. The asymptotic theory prediction of the vortices drift caused by interaction with sharp thickness variations in a layer has been confirmed in experiments with Belousov-Zhabotinski reaction, and verified in computer simulations with a variety of cell excitation models, from extremely simplified "conceptual" models to realistic ionic kinetics models, and for tissue geometries from artificial idealised geometries to a realistic anatomy of human atria. A better underestanding of this phenomenon may have significant implications in clinics, say for chosing an individual ablation strategy for treatment of atrial fibrillation.

Validation of the identified new phenomenon has so far been done only on a single model of human atrium, and understanding of to what extent the effect is universal requires extensive testing on a wide variety of cardiac MRI anatomy models, before experimental testing and clinical implications can be considered. The aim of the proposed project is to visit the Auckland Bioengineering Institute (ABI), New Zealand, which is an international leader in the heart and cardiovascular system research that combines instrumentation development, experimental measurements and modelling. ABI cardiovascular magnetic resonance (CMR) imaging group obtains most detail models of heart geometry and tissue microstructure. This visit will forge a closer collaboration than it is feasible from a distance, and provide a possibility of exhaustive testing of the new phenomenon in the most up-to-date anatomically and biophysically realistic models. An extra benefit will be provided by the applicant's participation in Cardiac Physiome Workshop (23 August 2016, Seoul, Korea), which will be a unique opportunity to discuss our recent findings and future directions of research with the world leaders in the field.

Planned Impact

- Direct beneficiaries of the overseas research visit will be the applicant's immediate research group at Liverpool, Exeter, Edinburgh, and other UK Universities, established as a result of our previous EPSRC funded projects, and the host Cardiac and Cardiovascular research groups at Auckland Bioengineering Institute (ABI).

Most important we see following groups of potential beneficiaries:
- Cardiac electrophysiology: experimentalists studying re-entrant arrhythmia in cell cultures, tissues, and animals;
- Researchers working in mathematical modelling of cardiac arrhythmias;
- Nonlinear science: researchers working in the theory and applications of excitable media and in the theory of other nonlinear self-organized dissipative structures;
- Applied mathematicians and software developers;
- Electrophysiology HE teachers and students;
- Nonlinear science HE teachers and students;
- Mathematical Biology HE teachers and students; and
- Computer Science HE teachers and students.
The above groups are immediate beneficiaries and are all academic.

Specific subsequent benefits depend on progress of research and therefore by necessity are speculative. For cardiological applications, following groups of beneficiaries may be envisaged:
- Biomedical industry that manufacture pacemakers, operating theatre and implantable defibrillators;
- Pharmaceutical industry that manufacture anti arrhythmic drugs;
- NHS, cardiac surgeons and clinicians in general;
- cardiac patients;
- general public.

Treatment and prevention of ventricular fibrillation, with 70,000-90,000 deaths related directly to it in the UK each year, with survival rates only 2%, is of utmost importance and is the subject of intensive research. Other types of arrhythmia, e.g. atrial fibrillation, may be less lethal but affect quality of life of a wider population and place a significant burden on the NHS. Any practical progress will therefore have significant impact on UK wellbeing, as well as economically:
- New operating theatre and implantable defibrillators and related employment in biomedical industry;
- New classes of anti-arrhythmic drugs and related employment in pharmaceutical industry;
- Better chronic and emergency treatment, lower mortality, lower hospital care costs;
- Economic implications for general public via lower unemployment, tax revenue from industries involved and lower NHS burden and prolongation of the active life of the ageing population.

All of this will enhance economic competitiveness of the UK, particularly, if the UK's leading role in relevant research is ensured.
 
Description Despite over a century study, the mechanisms of cardiac arrhythmias are poorly understood. Even modern experimental methods do not provide sufficient temporal and spacial resolution to trace down fine details of fibrillation development in samples of cardiac tissue, not to mention the heart in vivo. Advances in human genetics provide information on the impact of certain genes on cellular activity, but do not explain the resultant mechanisms by which fibrillation arises. Thus, for some genetic cardiac diseases, the first presenting symptom is death.

Combination of mathematical modelling and the latest realistic computer simulations of electrical activity in the heart have much advanced our understanding of heart fibrillation and sudden cardiac death, and the impact of in-silico modelling, or indeed in-silico "testing", is expected to increase significantly as we approach the ultimate goal of a patient whole-heart modelling.

Our recent progress in asymptotic analysis of dissipative vortices dynamics has revealed a new phenomenon of the vortices interaction with sharp variations of thickness in excitable layer. Such interaction of cardiac re-entry with sharp anatomical features, as e.g. pectinate muscles and terminal crest in atria, can cause considerable displacement of established localisation of re-entry compared to where it was first localised. A better understanding of this phenomenon will have significant implications in clinics, say for choosing an individual ablation strategy for treatment of atrial fibrillation.

The Auckland Bioengineering Institute (ABI) is the international leader in the heart and cardiovascular system research, developing all aspects of instrumentation, experimental measurements, modelling, and most importantly for the research project, ABI is the international leader in obtaining the most detail, down to a few microns resolution, models of heart geometry and tissue microstructure. This research visit to ABI has forged a close collaboration in progress, for the exhaustive testing of the new phenomenon in the most up-to-date anatomically and biophysically realistic models. The already obtained in collaboration with ABI, post-visit provisional results confirm e.g. the cardiac re-entry wave-particle duality behaviour in the Pulmonary Vein Wall which might have significant impact on the ablation strategies. Validation of the identified new phenomenon has now been done on a number of high resolution human and animal MRI- and micro-CT based computer models of the heart. It significantly enhanced our understanding of the role of anatomy of the heart, its geometry and structured anisotropy in cardiac arrhythmias and fatal fibrillation. Having said that, to what extent the effect is universal requires further extensive testing on a wide variety of cardiac MRI anatomy models, before experimental testing and clinical implications can be considered.

An extra benefit was from the PI's participation in
- Cardiac Physiome Workshop (23 August 2016, Seoul, Korea),
- Living Systems Institute workshop, Exeter, UK,
- Integrative Cardiac Dynamics program, KITP, UC Santa Barbara, USA,
which provided a unique opportunity to discuss our findings and future directions of research and collaboration with the world leaders in the field.
Exploitation Route So far, two years after the end of the project, apart from the established contact and collaboration with the Auckland Bioengineering Institute(ABI), the outcomes have been presented, often by a personal invitation and supported by overseas funders, at a number of influential conferences nationally and overseas. A major paper has been submitted for publication at Scientific Reports (Nature). It is already clear that all the objectives of the research visit to ABI have been fulfilled, and promise productive high impact collaboration with ABI. Direct beneficiaries of this collaboration will be the PI's immediate research group at Liverpool, Exeter, Edinburgh, Sheffield, and other UK Universities, established as a result of our previous EPSRC funded projects, and the Auckland Bioengineering Institute (ABI).

Immediate academic beneficiaries include
- Cardiac electrophysiology: experimentalists studying re-entrant arrhythmia in cell cultures, tissues, and animals;
- Researchers working in mathematical modelling of cardiac arrhythmias;
- Nonlinear science: researchers working in the theory and applications of excitable media and in the theory of other nonlinear self-organized dissipative structures;

For cardiological applications, the following beneficiaries are envisaged:
- Biomedical industry that manufacture pacemakers, operating theatre and implantable defibrillators;
- Pharmaceutical industry that manufacture anti arrhythmic drugs;
- NHS, cardiac surgeons and clinicians in general;
- cardiac patients;
- general public.
All of this will enhance economic competitiveness of the UK, particularly, if the UK's leading role in the relevant research is ensured.

The communication of deliverables is traditional, through the three interconnected routes: publication in open media (research journals and internet), presentations at specialist conferences, and personal contacts. Specific activities include:
• targeting most relevant and most read journals for publications: Journal of Electrocadiology, Biophys. J., Cardiovasc. Res., J. Amer. Physiol. Heart and Circ., J. Cardiovasc. Electrophysiol., J. Physiol., Phil. Trans. Roy. Soc. A and B, Proc. Roy. Soc. Lond. A and B. Where appropriate we will consider "free to read" options to enhance
circulation and impact of our results.
• seeking participation in appropriate meetings, e.g. CARDIOSTIM, FIMH, Computing in Cardiology, Physiome workshops, etc; as well as seeking knowledge transfer contacts with Biomedical and Pharmaceutical industry at the appropriate meetings, and Knowledge and Technology Transfer calls for proposals by RCUK and relevant charities.
• publicising the results on our personal and institutional websites and through mass media where appropriate.

The communication and engagement is currently delivered by the PI and the ABI collaborators team. Further funding will be crucial for the PI's impact activity, as University of Liverpool currently provides very limited support to the project.
Sectors Aerospace, Defence and Marine,Digital/Communication/Information Technologies (including Software),Financial Services, and Management Consultancy,Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology,Other

URL http://cgi.csc.liv.ac.uk/~ivb/projects
 
Description Despite over a century's study, the mechanisms of cardiac arrhythmias are poorly understood. Even modern experimental methods do not provide sufficient temporal and spacial resolution to trace down fine details of fibrillation development in samples of cardiac tissue, not to mention the heart in vivo. Advances in human genetics provide information on the impact of certain genes on cellular activity, but do not explain the resultant mechanisms by which fibrillation arises. Thus, for some genetic cardiac diseases, the first presenting symptom is death. Combination of mathematical modelling and the latest HPC anatomically realistic computer simulations of electrical activity in the heart have much advanced our understanding of heart fibrillation and sudden cardiac death, and the impact of in-silico modelling, or indeed in-silico "testing", is expected to increase significantly as we approach the ultimate goal of the whole-heart modelling. Our recent progress in asymptotic analysis of dissipative vortices dynamics has revealed a new phenomenon of the vortices interaction with sharp variations of thickness in excitable layer. Such interaction of cardiac re-entry with sharp anatomical features, as e.g. pectinate muscles and terminal crest in atria, can cause considerable displacement of established localisation of re-entry compared to where it was first localised. A better understanding of this phenomenon is to have significant implications in clinics, say for choosing of an individual ablation strategy for treatment of atrial fibrillation. Our in-silico comparative study of cardiac re-entry dynamics in DT-MRI based model of a human foetal heart confirmed the heart anatomy and anisotropy functional effect on cardiac re-entry self-termination as opposed to its sustainability, pinning to anatomical features, transition from pinned to anatomical re-entry, while the anisotropy of the tissue facilitates a re-entry self-termination. The research attracted close attention of the world leading researchers and clinicians. Our paper I.V. Biktasheva, R.A. Anderson, A.V. Holden, E. Pervolaraki, and F.C. Wen, "Cardiac re-entry dynamics & self-termination in DT-MRI based model of Human Foetal Heart", Frontiers Phys. 6:15, 2018. doi: 10.3389/fphy.2018.00015, attracted over 1,500 (fifteen hundred) views in just a year since its publication on 28/02/2018 http://loop-impact.frontiersin.org/impact/article/327090#totalviews/views, and is recognised as having "Above-average Attention Score compared to outputs of the same age (64th percentile)". The paper M. Antonioletti, V.N. Biktashev, A. Jackson, S.R. Kharche, T. Stary, I.V. Biktasheva, "BeatBox - HPC Simulation Environment for Biophysically and Anatomically Realistic Cardiac Electrophysiology", PLoS ONE 12(5): e0172292. https://doi.org/10.1371/journal.pone.0172292 2017, attracted over 1,600 (sixteen hundred) PLOS and PubMed Central page views and downloads in less than two years since its publication in May 2017.
First Year Of Impact 2018
Sector Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic,Policy & public services

 
Description EPSRC Overseas Travel grant EP/P008690/1 "Research Collaboration Visit to the Auckland Bioengineering Institute, New Zealand."
Amount £15,890 (GBP)
Funding ID EP/P008690/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2016 
End 11/2016
 
Description EPSRC POEMS Network Travel grant
Amount £750 (GBP)
Organisation University of Sheffield 
Sector Academic/University
Country United Kingdom
Start 08/2016 
End 09/2016
 
Description Invited Participation in KITP "Integrative Cardiac Dynamics" program, 25 June - 20 July 2018.
Amount $2,380 (USD)
Organisation University of California, Santa Barbara 
Sector Academic/University
Country United States
Start 06/2018 
End 07/2018
 
Description KITP " Integrative Cardiac Dynamics" Research Program, July 2018, Visitor grant supported by NSF Grant No. PHY-1748958, NIH Grant No. R25GM067110, and the Gordon and Betty Moore Foundation Grant No. 2919.01.
Amount $2,380 (USD)
Organisation Kavli Institute For Theoretical Physics 
Sector Academic/University
Country United States
Start 06/2018 
End 07/2018
 
Title BeatBox 
Description BeatBox, RRID:SCR_015780 -- HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology. 
Type Of Material Improvements to research infrastructure 
Year Produced 2013 
Provided To Others? Yes  
Impact In just 10 months from publication in PLoS ONE in May 2017 up to February 2018, there was 1,231 views of the paper. 
URL https://zenodo.org/badge/latestdoi/74274605
 
Description Cardiac re-entry in Human Foetal Heart 
Organisation University of Edinburgh
Department MRC Centre for Reproductive Health
Country United Kingdom 
Sector Academic/University 
PI Contribution Joint research on anatomically realistic computer simulation of cardiac re-entry dynamics and self-termination in DT-MRI based model of Human Foetal Heart.
Collaborator Contribution Joint research on anatomically realistic computer simulation of cardiac re-entry dynamics and self-termination in DT-MRI based model of Human Foetal Heart.
Impact Multidisciplinary collaboration involved MRC Centre for Reproductive Health, University of Edinburgh, School of Biomedical Science, University of Leeds, Department of Computer Science, University of Liverpool, and CEMPS, University of Exeter. Output: I.V. Biktasheva, R.A. Anderson, A.V. Holden, E. Pervolaraki, and F.C. Wen, "Cardiac re-entry dynamics & self-termination in DT-MRI based model of Human Foetal Heart", Frontiers Phys. 6:15, 2018. doi: 10.3389/fphy.2018.00015
Start Year 2015
 
Description EPSRC POEMS Network Travel grant, University of Sheffield, UK 
Organisation University of Sheffield
Department Faculty of Engineering
Country United Kingdom 
Sector Academic/University 
PI Contribution Research visit to the Auckland Bioengineering Institute, University of Auckland, August- September 2016.
Collaborator Contribution £750 towards the cost of Research visit to the Auckland Bioengineering Institute, University of Auckland, August- September 2016.
Impact Research visit to the Auckland Bioengineering Institute, University of Auckland, August- September 2016.
Start Year 2016
 
Description Exeter 
Organisation University of Exeter
Country United Kingdom 
Sector Academic/University 
PI Contribution joint research, participation in and organisation of mini symposia, joint funding applications
Collaborator Contribution joint research, participation in and organisation of mini symposia, joint funding applications
Impact Grant applications 1. EPSRC Grant application EP/L005387/1 "Meander and drift of spiral and scroll waves", 2013. 2. EPSRC project EP/K038915/1"BeatBox - HPC Environment for Biophysically and Anatomically Realistic Cardiac Simulations", 2010. 3. BBSRC grant application "BB/L018349/1 "HPC simulation environment for high-resolution intracellular Ca dynamics", 2013. Papers I. V. Biktasheva, H. Dierckx, and V. N. Biktashev, "Drift of scroll waves in thin layers caused by thickness features", submitted to Phys Rev Lett, 2014. arXiv:1408.3654 [nlin.PS] 2. Sanjay R. Kharche, Irina V. Biktasheva, Gunnar Seemann, Henggui Zhang, and Vadim N. Biktashev, "Anatomy Induced Drift of Spiral Waves in the Human Atrium", submitted to BMRI, 2014. 3. Vadim N. Biktashev, Irina V. Biktasheva, "Dynamics of filaments of scroll waves", in Engineering of Chemical Complexity II, eds. A.S.Mikhailov and G.Ertl, pp 221-238, World Scientific, Singapore, 2014. arXiv:1403.6654v1 [nlin.PS] 4. S.R. Kharche, I.V. Biktasheva, H.G. Zhang, and V.N. Biktashev, "Simulating the Role of Anisotropy in Human Atrial Cardioversion", The 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'13), Osaka, Japan, IEEE Engineering in Medicine and Biology Society, pp 6838-41, 2013. 5. S.R. Kharche, J. Beling, I.V. Biktasheva, H.G. Zhang, and V.N. Biktashev, "Simulating Cell Apoptosis Induced Sinus Node Dysfunction", The 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'13), Osaka, Japan, IEEE Engineering in Medicine and Biology Society, pp 6842-5, 2013. 6. S.R. Kharche, T. Stary, I.V. Biktasheva, H. Zhang, and V.N. Biktashev, "Computer simulation of the role of fibre orientation in cardioversion of chronic atrial fibrillation", Journal of Electrocardiology 46(4), e6-e7I, 2013. 7. I.V. Biktasheva, N A. Sarvazyan, and V.N. Biktashev, "Dynamics of Scroll Waves of Excitation in a Mathematical Model of Ischaemic Border Zone" , COMPUTING IN CARDIOLOGY, 39:445-448, 2012. 8. S. Kharche, I. Biktasheva, G. Seemann, H. Zhang, and V. Biktashev, "Cardioversion Using Feedback Stimuli in Human Atria" , COMPUTING IN CARDIOLOGY, 39:133-136, 2012. Conference/Minisymposia 1. Mini symposium "Dynamics of Spiral Waves - Parts I and II", SIAM CONFERENCE ON APPLICATIONS OF DYNAMICAL SYSTEMS 2013 (DS13), Snow Bird, Utah, USA. 2. Minisymposium "Dynamics of Spiral and Scroll Waves in Cardiac Tissue", SIAM CONFERENCE ON Nonlinear Waves and Coherent Structures 2014 (DS14), Cambridge, UK.
Start Year 2012
 
Description Leeds 
Organisation University of Leeds
Department School of Biomedical Sciences
Country United Kingdom 
Sector Academic/University 
PI Contribution joint research and research outputs, joint funding application
Collaborator Contribution joint research and research outputs, joint funding application
Impact 1. BBSRC grant application BB/L018640/1 HPC simulation environment for high-resolution intracellular Ca2+ dynamics Papers 1. Kharche SR; Stary T; Colman MA; Biktasheva IV; Workman AJ; Rankin AC; Holden AV; Zhang HG, "Effects of human atrial ionic remodelling by beta-blocker therapy on mechanisms of atrial fibrillation: a computer simulation", EUROPACE, Volume: 16 Issue: 10 Pages: 1524-1533, 2014 2. I.V. Biktasheva, V.N. Biktashev, and A.V. Holden, "Localization of response functions of spiral waves in the FitzHugh-Nagumo system", Int. J. Bifurcation & Chaos, vol 16, No.5, pp 1547-1555, 2006. 3. I.V. Biktasheva, V.N. Biktashev, and A.V. Holden, "Wave-breaks and self-termination of spiral waves in a model of human atrial tissue", Lecture Notes in Computer Science 3504: 293-303, 2005. 4. I.V. Biktasheva, V.N. Biktashev, W.N. Dawes, A.V. Holden, R.C. Saumarez and A.M.Savill "Dissipation of the excitation front as a mechanism of self-terminating arrhythmias", Int. J. Bifurcation & Chaos, Vol. 13, No. 12, pp.3645-3655, 2003. 5. I.V. Biktasheva, A.V. Holden and H. Zhang, "Stability, period and meander of spiral waves in two human virtual atrial tissues", J Physiol (Lond) , 544P, S067, 2002 6. V.N. Biktashev, I.V. Biktasheva, A.V. Holden, M.A. Tsyganov, J. Brindley, N.A. Hill "Spatiotemporal irregularity in an excitable medium with shear flow", Phys. Rev. E 60(2): 1897-1900, 1999
 
Description Research Collaboration Visit to the Auckland Bioengineering Institute, New Zealand. 
Organisation University of Auckland
Department Auckland Bioengineering Institute (ABI)
Country New Zealand 
Sector Academic/University 
PI Contribution Research Collaboration Visit to the Auckland Bioengineering Institute, New Zealand.
Collaborator Contribution host for Research Collaboration Visit to the Auckland Bioengineering Institute, New Zealand.
Impact Invited Lecture "Wave-particle duality of dissipative vortices and implications for cardiology" (Video http://www.abi.auckland.ac.nz/en/about/events/2016/wave-particle-duality-of-dissipative-vortices-and-implications-f.html) , in Auckland Bioengineering Institute seminar series , 30 August 2016, University of Auckland, New Zealand.
Start Year 2016
 
Description The George Washington University 
Organisation George Washington University
Country United States 
Sector Academic/University 
PI Contribution Joint research and joint research output
Collaborator Contribution Joint research and joint research output
Impact 1. I.V. Biktasheva, N A. Sarvazyan, and V.N. Biktashev, "Dynamics of Scroll Waves of Excitation in a Mathematical Model of Ischaemic Border Zone" , COMPUTING IN CARDIOLOGY, 39:445-448, 2012. 2. V.N. Biktashev, I.V. Biktasheva and N A. Sarvazyan, "Evolution of spiral and scroll waves of excitation in a mathematical model of ischaemic border zone", PLoS ONE 6(9): e24388, 2011. doi:10.1371/journal.pone.0024388
Start Year 2011
 
Description University of California Santa Barbara 
Organisation University of California, Santa Barbara
Country United States 
Sector Academic/University 
Start Year 2006
 
Title BeatBox 
Description BeatBox-HPC simulation environment for biophysically and anatomically realistic cardiac electrophysiology 
Type Of Technology Software 
Year Produced 2013 
Open Source License? Yes  
Impact In just 10 months since publication in PLoS One in May 2017, to February 2018, it had 1,231 total PLOS and PubMed Central page views and downloads. 
URL https://doi.org/10.1371/journal.pone.0172292
 
Title BeatBox - HPC Simulation Environment for Biophysically and Anatomically Realistic Cardiac Electrophysiology 
Description BeatBox is a High-Performance Computing (MPI) unified cardiac simulation environment that can be used to perform biophysically and anatomically realistic cardiac simulations. BeatBox provides: - A script interpreter to allow flexibility in setting up numerical experiments, thus eliminating the requirement to manipulate low level code and lengthy recompilations each time the simulation schedule is altered or a new simulation is constructed; - Serial and parallel (MPI) simulations; - A collection of ODE solvers; - A collection of finite differences PDE solvers for isotropic and anisotropic tissue models on regular and irregular boundary domains; - A major selection of CellML cardiac models and other excitable media models; - Multi-scale tissue modelling: 0-dimensional individual cell simulation, 1-dimensional fibre, 2-dimensional sheet and 3-dimensional slab of tissue, up to anatomically realistic whole heart simulations using the provided tissue model repository. - Run time measurements including tip tracing, filament tracing, ECG, samples of any variables; - Extensibility: one can easily plug in one's own solvers as well as cell kinetics models and tissue models (e.g. MRI finite difference meshes) into BeatBox's highly structured code. 
Type Of Technology Software 
Year Produced 2013 
Open Source License? Yes  
Impact Beatbox software was a direct output of 1) EPSRC project EP/I029664/1 "BeatBox - HPC Environment for Biophysically and Anatomically Realistic Cardiac Simulations"; 2) Liverpool University RDF Grant "Virtual Tissue Engineering: Software development for realistic computer simulation of cardiac activity on a Cluster of Parallel Processors". The underpinning research has been published in a number of publications, most notably in: Mario Antonioletti, Vadim N. Biktashev, Adrian Jackson, Sanjay R. Kharche, Tomas Stary, Irina V. Biktasheva, "BeatBox - HPC Simulation Environment for Biophysically and Anatomically Realistic Cardiac Electrophysiology", PLoS ONE 12(5): e0172292. https://doi.org/10.1371/journal.pone.0172292 2017. The 1st Beatbox Users workshop took place at the University of Manchester, UK, 24-25 June, 2013. BeatBox is already in use by researchers in UK, Belgium, Germany, New Zealand, etc. The (potential) impact includes: - Nonlinear science: researchers working in the theory and applications of excitable media and in the theory of other nonlinear self-organized dissipative structures; - Applied mathematicians and software developers; - Researchers working in mathematical modelling of cardiac arrhythmias; - Cardiac electrophysiology: experimentalists studying re-entrant arrhythmia in cell cultures, tissues and animals; - companies that manufacture pacemakers, operating theatre and implantable defibrillators; - pharmaceutical companies that manufacture anti-arrhythmic drugs, who will develop new classes of drugs based on the new understanding of the dynamics of cardiac arrhythmia; - clinicians and the NHS, who will have new more efficient methods of treatment of cardiac arrhythmia at their disposal, with fewer harmful side-effects, and lower treatment and care costs; - cardiac patients, whose life expectancy and quality of life will improve; - general public. Treatment and prevention of ventricular fibrillation, with 70,000-90,000 deaths related directly to it each year in the UK and with survival rates only 2%, is of utmost importance and is the subject of intensive research. Other types of arrhythmia, e.g. atrial fibrillation, may be less lethal but affect quality of life of a wider population and place a significant burden on the NHS. Any practical progress will therefore have significant impact on UK wellbeing, as well as economically: - New operating theatre and implantable defibrillators and related employment in biomedical industry; - New classes of anti-arrhythmic drugs and related employment in pharmaceutical industry; - Better chronic and emergency treatment, lower mortality, lower hospital care costs; - Economic implications for general public via lower unemployment, tax revenue from industries involved and lower NHS burden and prolongation of the active life of the ageing population. All of this will enhance economic competitiveness of the UK particularly if the UK's leading role in relevant research is ensured. 
URL https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0172292
 
Title DXSpiral: code for studying spiral waves on a disk 
Description DXSpiral is a toolkit for spiral waves in a disk, on a polar grid. The primary purpose is calculation of response functions (critical eigenmodes of the adjoint linearized operator), but the toolkit includes other components which can be useful independently. Principal algorithms are described in 1) Biktasheva, D.Barkley, V.N. Biktashev, G.V. Bordyugov, and A.J. Foulkes, "Computation of the response functions of spiral waves in active media" , Phys Rev E , 79, 056702, 2009. 2) I.V. Biktasheva, D.Barkley, V.N. Biktashev, and A.J. Foulkes, "Computation of the Drift Velocity of Spiral Waves using Response Functions" , Phys Rev E , 81, 066202, 2010. he above authors. 
Type Of Technology Software 
Year Produced 2010 
Open Source License? Yes  
Impact The DXSpiral software is a direct output of the EPSRC project EP/D074789/1 "Response functions for drift of spiral and scroll waves". The underpinning research has been published in a number of publications on macroscopic dissipative wave-particle duality of spiral waves dynamics, and computation of the Response Functions (RFs) of spiral waves. The new phenomenon of dissipative vortices interaction with fluctuation of thickness in a layer was predicted in the high impact publication: I. V. Biktasheva, H. Dierckx, and V. N. Biktashev, "Drift of scroll waves in thin layers caused by thickness features: Asymptotic theory and numerical simulations", Phys Rev Lett, 114, 068302, 2015. DXSpiral is already in use by colleagues in UK (Warwick), Belgium (Gent) and USA (Florida State University, The George Washington University, and others), who works on the theory of spiral and scroll waves, nonlinear self-organised dissipative structures, and cardiac electrophysiology. The (potential) impact includes: - Cardiac electrophysiology: researchers working in experimental studies of re-entrant arrhythmias and their mathematical modelling. - Public health and wealth creation: long-term potential beneficiaries will be companies that manufacture pacemakers, operating theatre and implantable defibrillators, anti-arrhythmic drugs, and hence eventually patients and general public. - Dissipative vortices in atmospheric layer: influence of hurricanes' dynamics on Climate and Weather. 
URL https://cgi.csc.liv.ac.uk/~ivb/SOFTware/DXSpiral.html
 
Description Invited Talk "Cardiac re-entry dynamics in MRI- and micro-CT based models of the heart": given on 6th July 2018, for "Integrative Cardiac Dynamics" Research Program in Kavli Institute for Theoretical Physics, University of California, Santa Barbara, USA. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited Talk "Cardiac re-entry dynamics in MRI- and micro-CT based models of the heart" was given at the "Integrative Cardiac Dynamics Research Program" http://online.kitp.ucsb.edu/online/cardio18/ , on 6th July 2018, at the Kavli Institute for Theoretical Physics, University of California, Santa Barbara, USA.
Year(s) Of Engagement Activity 2018
URL http://online.kitp.ucsb.edu/online/cardio18/biktasheva/
 
Description Invited Talk "Spiral Waves": given on 1st July 2019, at "50 years of Excitable Media: from Theory to Applications" International Symposium, Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited Talk "Spiral Waves": given on 1st July 2019, at "50 years of Excitable Media: from Theory to Applications" International Symposium, Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.
Year(s) Of Engagement Activity 2019
URL https://emfta2019.excitablemedia.org./#hero
 
Description Invited Talk "Wave-particle duality of dissipative vortices and its implications for cardiology": given on 5th December 2018, at "Spiral waves and cardiac arrhythmias" International Workshop, Living Systems Institute, University of Exeter, UK. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Invited Talk "Wave-particle duality of dissipative vortices and its implications for cardiology": given on 5th December 2018, at "Spiral waves and cardiac arrhythmias" International Workshop, Living Systems Institute, University of Exeter, UK.
Year(s) Of Engagement Activity 2018
 
Description Lecture "Wave-particle duality of dissipative vortices and implications for cardiology", in Auckland Bioengineering Institute seminar series , 30 August 2016, University of Auckland, New Zealand. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Invited Lecture "Wave-particle duality of dissipative vortices and implications for cardiology" (Video http://www.abi.auckland.ac.nz/en/about/events/2016/wave-particle-duality-of-dissipative-vortices-and-implications-f.html) ,
in Auckland Bioengineering Institute seminar series , 30 August 2016, University of Auckland, New Zealand.
Year(s) Of Engagement Activity 2016
URL http://www.abi.auckland.ac.nz/en/about/events/2016/wave-particle-duality-of-dissipative-vortices-and...