25 Nov 2019
Quanyue Zhang was awarded a Richardson Travel Bursary to attend a research trip to meet Professor Raúl Conejeros at Pontificia Universidad Católica de Valparaíso in Chile. Here he tells us about the opportunity to collaborate with Prof Conejeros and Dr Scott, who share the same research interests, and exchange ideas on research projects as well as attending the Metabolic Modelling and Simulation Workshop.
‘I just finished my first year as a PhD student in the department of Chemical Engineering and Biotechnology at the University of Cambridge. My PhD project involves the modelling, control and optimisation of the dynamic process with mixed-culture microorganisms. More specifically, via modelling tools, I develop algorithms that can predict how microorganisms would behave and interact with each other in an industrial scale batch (or fed-batch) reactor.
‘My PhD supervisor, Dr Vassilios Vassiliadis, is a prominent member of Process System Engineering (PSE), contributing hugely in the field of system modelling and control. In order for me to gain information from the biology perspective, Dr Vassiliadis liaised Prof Raúl Conejeros from the Pontifical Catholic University of Valparaiso (PCUV) in Chile to discuss a potential collaboration between his group and myself. Prof Conejeros’s research interests on metabolic modelling and control strategies, as well as sensitivity analysis of microbial systems overlap with mine. He has extraordinary experience in biochemical engineering, both through academic research activities as well as interfacing with industry. Prof Conejeros and his research group specialise in novel biochemical technologies which are highly relevant to my current PhD research work on optimal control of dynamic biochemical processes. The current work on Dynamic Flux Balance Analysis (DFBA) that has been published in 2018 by Dr Vassiliadis, Dr Felipe Scott from the University of the Andes Chile, and Prof Conejeros constitutes a significant contribution towards the modelling of such challenging biological systems. Their paper successfully addressed the issue of solving large-scale the DFBA model accurately and smoothly, using Interior Point Method (IPM), which enables online control of the bioprocessing system. After a short discussion with Prof Conejeros this February, I went to PCUV to meet with Prof Conejeros and Dr Scott in July to discuss further improve on the IPM on the more complex microbial communities, partially funded by the Richardson Travel Bursary from Society of Chemical Industry (SCI). I am convinced that a collaboration with the research groups in Chile of novel biofuel and bioproduct sectors, producing reliable and flexible models that can be used by bioprocess industries both in the UK and in Chile.
‘During the visiting to PCUV, I had the opportunity to meet and interact extensively with Prof Conejeros to discuss novel optimal control strategies for microbial communities, and to exchange ideas on research topics, i.e. how reliable my model is in simulating mixed-culture systems, and how to carry out sensitivity analysis of these systems. The result of the sensitivity analysis of the biological system can lead to a modelling framework to spot the “bottleneck” (i.e. the rate-limiting step in a series of reactions) of the intricate biochemical system and find an alternative reaction pathway to circumvent it so as to maximise production rate or production yield. What is more, the result of the sensitivity analysis bears value in “model-based genetic engineering” which in the future can be used to predict how to genetically modify microorganisms. Dr Scott also contributed in the model which will be included in my first paper(s) planned to be submitted at the end of this year. I believe the meeting with both Prof Conejeros and Dr Scott is vital for my current research and it pointed me to the right direction for my PhD.
‘What is more, I had the opportunity of attend the Metabolic Modelling and Simulation Workshop on the 23rd of July. There were more than fifty scholars in the field of metabolic modelling who attended this workshop, including Dr Pedro Saa (The Pontifical Catholic University of Chile), Dr Ignacio Poblete (The Andrés Bello National University), and Dr David Tourigny (Columbia University). Invited speakers are giving enthralling talks in the field of metabolic modelling. Prof Saa’s Bayesian method on kinetic models triggered me as how to capture the biological heterogeneity of microbial population. Dr Tourigny has recently developed a DFBA modelling package on Python – as currently, we are modelling on MATLAB – which would be attractive for me in my later research work; he also proposed that the resource allocation in the microbial communities followed the basis of maximum entropy principle, which is insightful.
‘Though I hadn’t prepared for presentation, I engaged with the speakers after the talks and they all showed interest in what I am working on. To my surprise, they are all willing to hear my PhD project in detail and share their ideas on future directions. Dr Poblete was keen to collaborate with my group to investigate the simulation of more complex microbial system with more than 10 species; Dr Tourigny also expressed interest in collaboration with Prof Conejeros, Dr Scott and myself as well.
‘Besides, Chilean is an exquisite country. I had the fortune to visit some places during my stay there. Valparaiso’s street art is fascinating. I chatted with the locals and got to know a bit about their culture and history. My time in Chile was an enjoyable one.
‘I was very grateful to have this visiting scholar opportunity. It wouldn’t had been possible without SCI awarding me the Richardson Travel Bursary scheme of £850. I would sincerely like to thank the SCI community. This bursary provided me an opportunity to interact and connect with expert in this field. The first-hand discussion and ideas exchanged will be a driving force for carrying my research in the future. Finally, I would like to thank Dr Vassiliadis, Prof Raúl Conejeros, and Dr Felipe Scott for organising this meeting.’
Qianyue Zhang
PhD student
University of Cambridge
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