Author Archives: Eann Patterson

Spatial-temporal models of protein structures

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For a number of years I have been working on methods for validating computational models of structures [see ‘Model validation‘ on September 18th 2012] using the full potential of measurements made with modern techniques such as digital image correlation [see ‘256 shades of grey‘ on January 22nd 2014] and thermoelastic stress analysis [see ‘Counting photons to measure stress‘ on November 18th 2015].  Usually the focus of our interest is at the macroscale, for example the research on aircraft structures in the MOTIVATE project; however, in a new PhD project with colleagues at the National Tsing Hua University in Taiwan, we are planning to explore using our validation procedures and metrics [1] in structural biology.

The size and timescale of protein-structure thermal fluctuations are essential to the regulation of cellular functions. Measurement techniques such as x-ray crystallography and transmission electron cryomicroscopy (Cryo-EM) provide data on electron density distribution from which protein structures can be deduced using molecular dynamics models. Our aim is to develop our validation metrics to help identify, with a defined level of confidence, the most appropriate structural ensemble for a given set of electron densities. To make the problem more interesting and challenging the structure observed by x-ray crystallography is an average or equilibrium state because a folded protein is constantly in motion undergoing harmonic oscillations, each with different frequencies and amplitude [2].

The PhD project is part of the dual PhD programme of the University of Liverpool and National Tsing Hua University.  Funding is available in form of a fee waiver and contribution to living expenses for four years of study involving significant periods (perferably two years) at each university.  For more information follow this link.

References:

[1] Dvurecenska, K., Graham, S., Patelli, E. & Patterson, E.A., A probabilistic metric for the validation of computational models, Royal Society Open Society, 5:180687, 2018.

[2] Justin Chan, Hong-Rui Lin, Kazuhiro Takemura, Kai-Chun Chang, Yuan-Yu Chang, Yasumasa Joti, Akio Kitao, Lee-Wei Yang. An efficient timer and sizer of protein motions reveals the time-scales of functional dynamics in the ribosome (2018) https://www.biorxiv.org/content/early/2018/08/03/384511.

Image: A diffraction pattern and protein structure from http://xray.bmc.uu.se/xtal/

Digitally-enabled regulatory environment for fusion powerplants

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Digital twins are a combination of computational models and real-world data describing the form, function and condition of a system [see ‘Can you trust your digital twin?‘ on November 23rd 2016]. They are beginning to transform design processes for complex systems in a number of industries.  We have been working on a proof-of-concept study for a digital reactor in fission energy based on the Integrated Nuclear Digital Environment (INDE) [1].  The research has been conducted by the Virtual Engineering Centre (VEC) at the University of Liverpool together with partners from industry and national laboratories with funding from the UK Government for nuclear innovation.  In parallel, I having been working with a colleague at the University of Manchester and partners at the Culham Centre for Fusion Energy on the form of a digital environment for fusion energy taking account of the higher order of complexity, the scale of resources, the integration of novel technologies, and the likely diversity and distribution of organisations involved in designing, building and operating a fusion powerplant.  We have had positive interactions with the regulatory authorities during the digital fission reactor project and the culture of enabling-regulation [2] offers an opportunity for a new paradigm in the regulation of fusion powerplants.  Hence, we propose in a new PhD project to investigate the potential provided by the integration of digital twins with the regulatory environment to enable innovation in the design of fusion powerplants.

The PhD project is fully-funded for UK and EU citizens as part of a Centre for Doctoral Training and will involve a year of specialist training followed by three years of research.  For more information following this link.

References:

[1] Patterson EA, Taylor RJ & Bankhead M, A framework for an integrated nuclear digital environment, Progress in Nuclear Energy, 87:97-103, 2016.

[2] http://www.onr.org.uk/documents/2018/guide-to-enabling-regulation-in-practice.pdf

Image: https://www.pexels.com/photo/diagram-drawing-electromagnetic-energy-326394/

Crack tip plasticity in reactor steels

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Amplitude of temperature in steel due to a cyclic load with a crack growing from left to right along the horizontal centre line with the stress concentration at its tip exhibiting the peak values. The wedge shapes in the left corners are part of the system.

At this time of year the flow into my inbox is augmented daily by prospective PhD students sending me long emails describing how their skills, qualifications and interests perfectly match the needs of my research group, or sometimes someone else’s group if they have not been careful in setting up their mass mailing.  At the moment, I have four PhD projects for which I am looking for outstanding students; so, because it will help prospective students and might interest my other readers but also because I am short of ideas for the blog, I plan to describe one project per week for the next month.

The first project is about the effect of hydrogen on crack tip plasticity in reactor steels.  Fatigue cracks grow in steels by coalescing imperfections in the microstructure of the material until small voids are formed in areas of high stress.  When these voids connect together a crack is formed.  Repeated loading and unloading of the material provides the energy to move the imperfections, known as dislocations, and geometric features in structures are stress concentrators which focus this energy causing cracks to be formed in their vicinity.  The movement of dislocations causes permanent, or plastic deformation of the material.  The sharp geometry of a crack tip becomes a stress concentrator creating a plastic zone in which dislocations pile up and voids form allowing the crack to extend [see post on ‘Alan Arnold Griffith‘ on April 26th, 2017].  It is possible to detect the thermal energy released during plastic deformation using a technique known as thermoelastic stress analysis [see ‘Counting photons to measure stress‘ on November 18th 2015] as well as to measure the stress field associated with the propagating crack [1].  One of my current PhD students has been using this technique to investigate the effect of irradiation damage on the growth of cracks in stainless steel used in nuclear reactors.  We use an ion accelerator at the Dalton Cumbrian Facility to introduce radiation damage into specimens the size of a postage stamp and afterwards apply cyclic loads and watch the fatigue crack grow using our sensitive infra-red cameras.  We have found that the irradiation reduced the rate of crack growth and we will be publishing a paper on it shortly [and a PhD thesis].  In the new project, our industrial sponsors want us to explore the effect of hydrogen on crack growth in irradiated steel, because the presence of hydrogen is known to accelerate fatigue crack growth [2] which is believe to happen as a result of hydrogen atoms disrupting the formation of dislocations at the microscale and localising plasticity at crack tip on the mesoscale.  However, these ideas have not been demonstrated in experiments, so we plan to do this using thermoelastic stress analysis and to investigate the combined influence of hydrogen and irradiation by developing a process for pre-charging the steel specimens with hydrogen using an electrolytic cell and irradiating them using the ion accelerator.  Both hydrogen and radiation are present in a nuclear reactor and hence the results will be relevant to predicting the safe working life of nuclear reactors.

The PhD project is fully-funded for UK and EU citizens as part of a Centre for Doctoral Training and will involve a year of specialist training followed by three years of research.  For more information following this link.

References:

  1. Yang, Y., Crimp, M., Tomlinson, R.A., Patterson, E.A., 2012, Quantitative measurement of plastic strain field at a fatigue crack tip, Proc. R. Soc. A., 468(2144):2399-2415.
  2. Matsunaga, H., Takakuwa, O., Yamabe, J., & Matsuoka, S., 2017, Hydrogen-enhanced fatigue crack growth in steels and its frequency dependence. Phil. Trans. R. Soc. A, 375(2098), 20160412

Is there a real ‘you’ or ‘I’?

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I have written recently about time and consciousness [see ‘Time at the heart of our problems‘ on January 30th, 2019 and ‘Limits of imagination‘ on February 13th, 2019].  We perceive some things as almost constant or changeless, such as trees and landscapes; however, that is just a consequence of our perception of time.  Nothing that is in equilibrium, and hence unchanging, can be alive.  The laws of thermodynamics tell us that disequilibrium is fundamental in driving all processes including life.  Our perception of experience arises from registering changes in the flow of sensory information to our brains and as well as changes in the networks of neurons in our brains.  Hence, both time and complexity appear to be essential ingredients for consciousness. Even when we sit motionless watching an apparently unchanging scene, as a consequence of the endless motion of connections and signals in our brains, our minds are teeming with activity, churning through great jumbles of ideas, memories and thoughts.  Next time you are sitting quietly, try to find ‘you’; not the things that you do or experience but the elusive ‘I’.  We assume that the elusive ‘I’ is there, but most of us find nothing when we look for it.  Julian Baggini has suggested that the “I” is ‘a nothing, contentless centre around which experiences flutter like butterflies.’

Sources:

Baggini J, The pig that wants to be eaten and 99 other thought experiments, London: Granta Publications, 2008.

Czerski H, Storm in a teacup:the physics of everyday life, London: Penguin Random House, 2016.

Godfrey-Smith P, Other minds: the octopus and the evolution of intelligent life, London: William Collins, 2018.

Rovelli C, Seven brief lessons on physics, London, Penguin Books. 2016.