Tag Archives: NTHU

Spatial-temporal models of protein structures

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/

Press release!

A jumbo jet has about six million parts of which roughly half are fasteners – that’s a lot of holes.

It is very rare for one of my research papers to be included in a press release on its publication.  But that’s what has happened this month as a consequence of a paper being included in the latest series published by the Royal Society.  The contents of the paper are not earth shattering in terms of their consequences for humanity; however, we have resolved a long-standing controversy about why cracks grow from small holes in structures [see post entitled ‘Alan Arnold Griffith‘ on  April 26th, 2017] that are meant to be protected from such events by beneficial residual stresses around the hole.  This is important for aircraft structures since a civilian airliner can have millions of holes that contain rivets and bolts which hold the structure together.

We have used mechanical tests to assess fatigue life, thermoelastic stress analysis to measure stress distributions [see post entitled ‘Counting photons to measure stress‘ on November 18th, 2015], synchrotron x-ray diffraction to evaluate residual stress inside the metal and microscopy to examine failure surfaces [see post entitled ‘Forensic engineering‘ on July 22nd, 2015].  The data from this diverse set of experiments is integrated in the paper to provide a mechanistic explanation of how cracks exploit imperfections in the beneficial residual stress field introduced by the manufacturing process and can be aided in their growth by occasional but modest overloads, which might occur during a difficult landing or take-off.

The success of this research is particularly satisfying because at its heart is a PhD student supported by a dual PhD programme between the University of Liverpool and National Tsing Hua University in Taiwan.  This programme, which supported by the two partner universities, is in its sixth year of operation with a steady state of about two dozen PhD students enrolled, who divide their time between Liverpool, England and Hsinchu, Taiwan.  The synchrotron diffraction measurements were performed, with a colleague from Sheffield Hallam University, at the European Synchrotron Research Facility (ESRF) in Grenoble, France; thus making this a truly international collaboration.

Source:

Amjad K, Asquith D, Patterson EA, Sebastian CM & Wang WC, The interaction of fatigue cracks with a residual stress field using thermoelastic stress analysis and synchrotron x-ray diffraction experiments, R. Soc. Open Sci. 4:171100.

Out and about

butterfly-with-branched-scrolls-vaseI have been away from Liverpool a lot in the last few weeks. Teaching in Manchester and London but also visiting Taiwan. In the capital, Taipei they have yellow cabs and a succession of black limos pick up visitors from the airport. I even saw a baseball pro shop but despite the strong American influence, the culture is definitely Chinese so ordering meals and buying train tickets is a challenge if you don’t speak or read Mandarin. I am a Visiting Professor at the National Tsing Hua University and was there to meet with some PhD students and participate in a research workshop on computational modelling [see my post on Can you trust your digital twins?on November 22nd, 2016]. It wasn’t my first trip to Taiwan [see my post entitled ‘Crash in Taipei: an engineer’s travelogue?’ on November 19th, 2014] but I visited a high school for the first time. I spent half a day meeting teachers and pupils at the Taipei European School. I gave a talk based on my post entitled ‘Happenstance, not engineering?’ [see my post on November 9th, 2016] to several groups of science pupils in an attempt to explain what engineers do. The reception was enthusiastic and we had some good question and answer sessions. It was a first for me to do this in any school and the first time in the memory of the teachers that a professional engineer had visited the school. A while ago I wrote about nurturing the spirit through the exchange of gifts in the form of knowledge [see my post entitled ‘Knowledge spheres’ on March 9th, 2016]. My spirits were lifted by talking to the pupils and maybe one or two of them will have been persuaded to think about becoming an engineer. We also exchanged material gifts so that I have a beautiful vase to stand on my shelf and remind me of an enjoyable visit and hopefully prompt me to go again. Lots of young people have no idea what engineers do and are looking for a career that will allow them to contribute to society, so they are surprised and excited when they realise engineering offers that opportunity. So, we should get out more and tell them about it.