Tag Archives: computational modelling

Aorta: structure to rupture

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Decorative image from a video showing predicted flow through aortic valve and resultant stress in leaflets of valveRegular readers have probably already realised that I have very broad interests in engineering from aircraft and power stations [see ‘Conversations about engineering over dinner and haircut‘ on February 16th, 2022] to nanoparticles interacting with cells [see ‘Fancy a pint of science‘ on April 27th, 2022].  So, it will come as no surprise to hear that I gave a welcome address to a workshop on ‘Aorta: Structure to Rupture‘ last week.  The workshop was organised in Liverpool by one of my colleagues, with sponsorship from the British Heart Foundation, and I was invited to welcome delegates in my capacity as Dean of the School of Engineering.  It was exciting on two levels: speaking, for the first time in more than two years, to an audience who had travelled from around the world to discuss research. And because the topic was closely associated with cardiac dynamics, which is a field that I worked in for nearly twenty years until around 2006.  I was part of an interdisciplinary team modelling the fluid-structure interaction in the aortic valve as it opens when blood is pumped through it by the heart and then closes to prevent back flow into the heart.  The team dispersed after I moved to the USA in 2004.  So speaking to the workshop last week was something of a trip down memory lane for me and led me to look up our last publication in the field.  I was surprised to find it was cited seven times last year.

The image in the thumbnail is a snapshot from a video showing the predicted time-varying distribution of blood flow through the aortic valve and the resultant distribution of stress in the leaflets of the valve during a heart beat.  The simultation is described in our last publication in cardiac dynamics: Carmody, C. J., Burriesci, G., Howard, I. C., & Patterson, E. A.,  An approach to the simulation of fluid–structure interaction in the aortic valve. J. Biomechanics, 39(1), 158-169, 2006.

Reduction in usefulness of reductionism

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decorative paintingA couple of months ago I wrote about a set of credibility factors for computational models [see ‘Credible predictions for regulatory decision-making‘ on December 9th, 2020] that we designed to inform interactions between researchers, model builders and decision-makers that will establish trust in the predictions from computational models [1].  This is important because computational modelling is becoming ubiquitous in the development of everything from automobiles and power stations to drugs and vaccines which inevitably leads to its use in supporting regulatory applications.  However, there is another motivation underpinning our work which is that the systems being modelled are becoming increasingly complex with the likelihood that they will exhibit emergent behaviour [see ‘Emergent properties‘ on September 16th, 2015] and this makes it increasingly unlikely that a reductionist approach to establishing model credibility will be successful [2].  The reductionist approach to science, which was pioneered by Descartes and Newton, has served science well for hundreds of years and is based on the concept that everything about a complex system can be understood by reducing it to the smallest constituent part.  It is the method of analysis that underpins almost everything you learn as an undergraduate engineer or physicist. However, reductionism loses its power when a system is more than the sum of its parts, i.e., when it exhibits emergent behaviour.  Our approach to establishing model credibility is more holistic than traditional methods.  This seems appropriate when modelling complex systems for which a complete knowledge of the relationships and patterns of behaviour may not be attainable, e.g., when unexpected or unexplainable emergent behaviour occurs [3].  The hegemony of reductionism in science made us nervous about writing about its short-comings four years ago when we first published our ideas about model credibility [2].  So, I was pleased to see a paper published last year [4] that identified five fundamental properties of biology that weaken the power of reductionism, namely (1) biological variation is widespread and persistent, (2) biological systems are relentlessly nonlinear, (3) biological systems contain redundancy, (4) biology consists of multiple systems interacting across different time and spatial scales, and (5) biological properties are emergent.  Many engineered systems possess all five of these fundamental properties – you just to need to look at them from the appropriate perspective, for example, through a microscope to see the variation in microstructure of a mass-produced part.  Hence, in the future, there will need to be an increasing emphasis on holistic approaches and systems thinking in both the education and practices of engineers as well as biologists.

For more on emergence in computational modelling see Manuel Delanda Philosophy and Simulation: The Emergence of Synthetic Reason, Continuum, London, 2011. And, for more systems thinking see Fritjof Capra and Luigi Luisi, The Systems View of Life: A Unifying Vision, Cambridge University Press, 2014.

References:

[1] Patterson EA, Whelan MP & Worth A, The role of validation in establishing the scientific credibility of predictive toxicology approaches intended for regulatory application, Computational Toxicology, 17: 100144, 2021.

[2] Patterson EA &Whelan MP, A framework to establish credibility of computational models in biology. Progress in biophysics and molecular biology, 129: 13-19, 2017.

[3] Patterson EA & Whelan MP, On the validation of variable fidelity multi-physics simulations, J. Sound & Vibration, 448:247-258, 2019.

[4] Pruett WA, Clemmer JS & Hester RL, Physiological Modeling and Simulation—Validation, Credibility, and Application. Annual Review of Biomedical Engineering, 22:185-206, 2020.

Credible predictions for regulatory decision-making

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detail from abstract by Zahrah ReshRegulators are charged with ensuring that manufactured products, from aircraft and nuclear power stations to cosmetics and vaccines, are safe.  The general public seeks certainty that these devices and the materials and chemicals they are made from will not harm them or the environment.  Technologists that design and manufacture these products know that absolute certainty is unattainable and near-certainty in unaffordable.  Hence, they attempt to deliver the service or product that society desires while ensuring that the risks are As Low As Reasonably Practical (ALARP).  The role of regulators is to independently assess the risks, make a judgment on their acceptability and thus decide whether the operation of a power station or distribution of a vaccine can go ahead.  These are difficult decisions with huge potential consequences – just think of the more than three hundred people killed in the two crashes of Boeing 737 Max airplanes or the 10,000 or so people affected by birth defects caused by the drug thalidomide.  Evidence presented to support applications for regulatory approval is largely based on physical tests, for example fatigue tests on an aircraft structure or toxicological tests using animals.  In some cases the physical tests might not be entirely representative of the real-life situation which can make it difficult to make decisions using the data, for instance a ground test on an airplane is not the same as a flight test and in many respects the animals used in toxicity testing are physiologically different to humans.  In addition, physical tests are expensive and time-consuming which both drives up the costs of seeking regulatory approval and slows down the translation of new innovative products to the market.  The almost ubiquitous use of computer-based simulations to support the research, development and design of manufactured products inevitably leads to their use in supporting regulatory applications.  This creates challenges for regulators who must judge the trustworthiness of predictions from these simulations.  [see ‘Fake facts & untrustworthy predictions‘ on December 4th, 2019]. It is standard practice for modellers to demonstrate the validity of their models; however, validation does not automatically lead to acceptance of predictions by decision-makers.  Acceptance is more closely related to scientific credibility.  I have been working across a number of disciplines on the scientific credibility of models including in engineering where multi-physics phenomena are important, such as hypersonic flight and fusion energy [see ‘Thought leadership in fusion energy‘ on October 9th, 2019], and in computational biology and toxicology [see ‘Hierarchical modelling in engineering and biology‘ on March 14th, 2018]. Working together with my collaborators in these disciplines, we have developed a common set of factors which underpin scientific credibility that are based on principles drawn from the literature on the philosophy of science and are designed to be both discipline-independent and method-agnostic [Patterson & Whelan, 2019; Patterson et al, 2021]. We hope that our cross-disciplinary approach will break down the subject-silos that have become established as different scientific communities have developed their own frameworks for validating models.  As mentioned above, the process of validation tends to be undertaken by model developers and, in some sense, belongs to them; whereas, credibility is not exclusive to the developer but is a trust that needs to be shared with a decision-maker who seeks to use the predictions to inform their decision [see ‘Credibility is in the eye of the beholder‘ on April 20th, 2016].  Trust requires a common knowledge base and understanding that is usually built through interactions.  We hope the credibility factors will provide a framework for these interactions as well as a structure for building a portfolio of evidence that demonstrates the reliability of a model. 

References:

Patterson EA & Whelan MP, On the validation of variable fidelity multi-physics simulations, J. Sound & Vibration, 448:247-258, 2019.

Patterson EA, Whelan MP & Worth A, The role of validation in establishing the scientific credibility of predictive toxicology approaches intended for regulatory application, Computational Toxicology, 17: 100144, 2021.

Image: Extract from abstract by Zahrah Resh.

My Engineering Day

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Photograph of roof tops and chimneys in Liverpool.Today is ‘This is Engineering’ day organised by the Royal Academy of Engineering to showcase what engineers and engineering really look like, celebrate our impact on the world and shift public perception of engineering towards an appreciation that engineers are a varied and diverse group of people who are critical to solving societal challenges.  You can find out more at https://www.raeng.org.uk/events/online-events/this-is-engineering-day-2020.  I have decided to contribute to ‘This is Engineering’ day by describing what I do on a typical working day as an engineer. 

Last Wednesday was like many other working days during the pandemic.  I got up about 7am went downstairs for breakfast in our kitchen and then climbed back upstairs to my home-office in the attic of our house in Liverpool [see ‘Virtual ascent of Moel Famau’ on April 8th, 2020].  I am lucky in that my home-office is quite separate from the living space in our house and it has a great view over the rooftops.  I arrived there at about 7.45am, opened my laptop, deleted the junk email, and dealt with the emails that were urgent, interesting or could be replied to quickly.  At around 8am, I closed my email and settled down to write the first draft of a proposal for funding to support our research on digital twins [see ‘Tacit hurdle to digital twins’ on August 26th, 2020].  I had organised a meeting earlier in the week with a group of collaborators and now I had the task of converting the ideas from our discussion into a coherent programme of research.  Ninety caffeine-fuelled minutes later, I had to stop for a Google Meet call with a collaborator at Airbus in Toulouse during which we agreed the wording on a statement about the impact our recent research efforts.  At 10am I joined a Skype call for a progress review with a PhD student on our dual PhD programme with National Tsing Hua University in Taiwan, so we were joined by his supervisor in Taiwan where it was 6pm [see ‘Citizens of the World’ on November 27th, 2019].  The PhD student presented some very interesting results on evaluating the waviness of fibres in carbon-fibre composite materials using ultrasound measurements which he had performed in our laboratory in Liverpool.  Despite the local lockdown in Liverpool due to the pandemic, research laboratories on our campus are open and operating at reduced occupancy to allow social distancing.

After the PhD progress meeting, I had a catch-up session with my personal assistant to discuss my schedule for the next couple of weeks before joining a MS-Teams meeting with a couple of colleagues to discuss the implications of our current work on computational modelling and possible future directions.  The remaining hour up to my lunch break was occupied by a conference call with a university in India with whom we are exploring a potential partnership.  I participated in my capacity as Dean of the School of Engineering and joined about twenty colleagues from both institutions discussing possible areas of collaboration in both research and teaching.  Then it was back downstairs for a half-hour lunch break in the kitchen. 

Following lunch, I continued in my role as Dean with a half-hour meeting with Early Career Academics in the School of Engineering followed by internal interviews for the directorship of one of our postgraduate research programmes.  At 3.30pm, I was able to switch back to being a researcher and meet with a collaborator to discuss the prospects for extending our work on tracking synthetic nanoparticles into monitoring the motion of biological entities such as viruses and bacteria [see ‘Modelling from the cell through the individual to the host population’ on May 5th 2020].  Finally, as usual, I spent the last two to three hours of my working day replying to emails, following up on the day’s meetings and preparing for the following day.  One email was a request for help from one of my PhD students working in the laboratory who needed a piece of equipment that had been stored in my office for safekeeping.  So, I made the ten-minute walk to campus to get it for her which gave me the opportunity to talk face-to-face with one of the post-doctoral researchers in my group who is working on the DIMES project [see ‘Condition-monitoring using infra imaging‘ on June 17th, 2020].  After dinner, my wife and I walked down to the Albert Dock and along the river front to Princes Dock and back up to our house.

So that was my Engineering Day last Wednesday!

 

Logos of Clean Sky 2 and EUThe DIMES project has received funding from the Clean Sky 2 Joint Undertaking under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 820951.  The opinions expressed in this blog post reflect only the author’s view and the Clean Sky 2 Joint Undertaking is not responsible for any use that may be made of the information it contains.