Education in Cambridge

2018-2022 Doctor of Philosophy in Physics (Ph.D.)

Optoelectronics Group, Cavendish Laboratory
Department of Physics, University of Cambridge, United Kingdom
Supervisor: Prof. Erika Eiser
Thesis Title: Multi-Level Coarse-Grained Modelling on DNA Functionalised Building Blocks
(View my PhD Thesis on Cambridge Apollo) (View my PhD Thesis in PDF)
Simulation Guide Book: Daan Frenkel and Berend Smit. "Understanding molecular simulation: from algorithms to applications", volume 1. Elsevier, 2001.
Simulation Mentor: Prof. Daan Frenkel

2016-2017 Master of Philosophy in Computational Biology (M.Phil.)

Department of Applied Mathematics, University of Cambridge, United Kingdom
Supervisor: Prof. Stephen J. Eglen

MPhil in Computational Biology program aims to bring together the fields of biological, mathematical, and physical sciences with the quantitative elements of contemporary biology and medicine, encompassing areas such as bioinformatics. Couses including: biological image analysis, computational neuroscience, genome informatics, statistics, probability and scientific programming etc. By uniting researchers and specialists from various academic departments and industry, this program fosters collaborative efforts to advance research in the analysis, understanding and use of data science and artificial intelligence (AI). Learn more

Education in Oxford

2017-2018 Master of Science in Nanotechnology for Medicine and Health Care (M.Sc./PGcert)

Department of Continuing Education, University of Oxford, United Kingdom
Supervisor: Dr. Christiane Norenberg ; Tutor: Prof. Peter Dobson OBE

Nanomedicine stands at the forefront of modern healthcare. Nanoparticles have emerged as a promising platform for drug delivery, enabling the extension of the patent life of drugs while significantly enhancing their targeting capabilities and therapeutic effectiveness. Nanoparticles have the potential to enhance various medical imaging techniques, and in certain cases, they can provide a combined approach for both diagnosis and therapy, known as 'theranostics'. Nanotechnology is serving as a foundation for numerous innovative regenerative medicine strategies, relying on artificial scaffold structures. It also presents solutions for the development of next-generation point-of-care biosensors and advanced gene sequencing instruments. By harnessing the power of nanotechnology, these cutting-edge applications are revolutionizing the fields of regenerative medicine, diagnostics, and genetic analysis. This course draws on the world-class research and teaching in nanotechnology and nanomedicine enable me to understand the principles of nanotechnology and its application in medical research and clinical practice.
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Education in Nottingham

2013-2016 Bachelor of Engineering with Honors in Electrical and Electronic Engineering (B.Eng)

Department of Engineering, University of Nottingham, United Kingdom
Supervisor: Prof. Stephen Morgan

My Bachelor degree focuses on equipping with the essential knowledge and skills in electrical engineering, enabling me to engage lab-based projects, both individually and in small teams, I developed critical problem-solving and design abilities. Electrical Engineering are responsible for the design and development of cutting-edge technologies used in power generation and processing as well as playing a vital role in distributing electrical energy, including the implementation of 'Smart Grid' technologies for renewable energy sources. This study paved the way for the advancement of Signal Processing and Communications, Power Electronic Applications and Control, Software Engineering and Programming ... etc. Learn more

Research Projects

DNA nanotechnology has proliferated as investigators have increasingly harnessed the selectivity of DNA base pairing to form multitudes of diverse structures, with a wide range of applications. My researches focusing on a multi-level strategy to demonstrate new horizons of coarse-grained simulation systems. With the service of this multi-level coarse-grained strategy, a more realistic simulation system can be devoted to illustrate more reliable physical properties.

DNA-Functionalised Triblock Copolymers: F108 Pluronics + DNA

Pluronics®are triblock copolymers (referred to as 'PEO-PPO-PEO') that have two hydrophilic polyethylene oxide (PEO) outer blocks and an inner block of polypropylene oxide (PPO) that is hydrophilic at low temperatures but becomes hydrophobic upon heating. These block copolymers are polymeric surfactants, commercially also known as Poloxamers®, and are widely used in lubrication, detergency, pharmaceuticals, foaming, emulsification and coating. In this projects, I built a coarse-grained simulation model with temperature-sensitive hydrophobic monomers to study the structure and phase behaviour of a symmetric bead-spring model for the PEO-PPO-PEO polymers. Further, we extended our model by adding a sticky patch to each free PEO chain, thus mimicking the complementary DNA sticky ends. This stickiness provides an additional, temperature dependent driving force for aggregation between two chain ends at low temperatures.

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Towards New Liquid Crystal Phases of DNA Mesogens

Liquid crystals play an essential role in biology because they combine order and mobility, offering a basic requirement for self-organisation and structure formation in all living systems. The ability of dsDNA to form LC phases when it is hydrate was first demonstrated in the 1940s. Since that time, the LC properties of aqueous suspensions of DNA have been extensively characterised. The geometry and physical characteristics of DNA are closely related to its chemical structure. In this research, I report on the second-level coarse-graining of the nunchucks DNA towards finding new liquid phase transitions. I did this work with Kit Gallagher as a day-to-day supervisor in his part III project. To begin with, we developed the LAMMPS code in single-stage, rigid-rod simulations to confirm that the analytical techniques could accurately recreate Onsager’s theory. Then we investigated a system of stiff rods and concentrated on the transition from the isotropic to the nematic phase.

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The Role of Flexible Joints in a Linker-Mediated DNA Hydrogel

DNA hydrogels are polymeric networks made entirely from DNA. The convenient programmability and multi-functional tunability of DNA make it a perfect material for constructing a three-dimensional structure in hydrogels. DNA hydrogels are also biocompatible and therefore useful for biomedical applications such as bio-sensing technology, targeted drug delivery, 3D bio-printing, regenerative medicine and tissue engineering. In this research, I reported numerical work using oxDNA to test the thermodynamic stability and topography of Y-shaped DNA nanostars connected via rigid, linear DNA-linkers. The specific DNA sequences we used were those we tested in experiments to study the formation of DNA hydrogels as function of temperature and DNA concentration. This work was done in collaboration with Dr. Iliya Stoev, who did most of the experiments in this project. Our dynamic light scattering (DLS) measurements showed that when inserting sufficiently long flexible ssDNA joints between the linear linker and the Y-shaped DNA we suppress gelation. This motivated me to test the effect of the length of the flexible joints.

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Determining the micellisation phase boundary for multiblock copolymers

Multiblock copolymers are creative building blocks in the repertoire of self-assembled polymeric micelles, with practical applications in nanoscience and biotechnology. Amongst the many different polymeric surfactants are the symmetric ABA-type triblock copolymers PEO-PPO-PEO. The micellisation of block copolymers in solutions is inherently complex as the critical micellisation temperature (CMT) increase with decreasing concentration. Even above the CMT, unimers, micelles and micellar aggregates coexist, and the relative proportion of each species depends strongly on the temperature and polymer concentration. The CMT can be determined experimentally by fluorescence spectroscopy, surface tension, solubilisation methods, light scattering and rheology. In simulations, the exact aggregation number of each micelle is known; hence a more direct method can be applied to investigate the unimer/micellar status in an equilibration period to determine the micellisation phase boundary.

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Publications

my_thesis

1. Jiaming Yu. "Multi-Level Coarse-Grained Modelling on DNA Functionalised Building Blocks." Apollo: doi.org/10.17863/CAM.93097 (2023)

2. Iliya D. Stoev, Tianyang Cao, Alessio Caciagli, Jiaming Yu , Christopher Ness, Ren Liu, Rini Ghosh, Thomas O'Neill, Dongsheng Liu and Erika Eiser. "On the role of flexibility in linker-mediated DNA hydrogels." Soft Matter 16.4: 990-1001. doi.org/10.1039/C9SM01398A. (2020)

3. Kit Gallagher, Jiaming Yu, Ren Liu, David A. King and Erika Eiser. "Towards New Liquid Crystal Phases of DNA mesogens." arXiv preprint arXiv:2302.03501 (2023)

4. Ren Liu, Jiaming Yu, Xiaojing Tang, Rini Ghosh and Erika Eiser, "Dynamic Light Scattering based microrheology of End-functionalised triblock copolymer solutions." Polymers 15.3: 481 (2022)

5. Jiaming Yu, Eivind Bering, Ren Liu and Erika Eiser. "Numerical study of pluronics with DNA-functionalised triblock copolymer system." link here (In paraperation)

...

Developments

2019 oxDNA Workshop, Beecroft Building, Department of Physics, University of Oxford.
The workshop held in Oxford from September 2019. The aim of the workshop is to bring together both developers and users of the oxDNA and oxRNA models not only to share current research projects, but also to set the agenda for the future development of the oxDNA and oxRNA models, code and infrastructure. Particular to advance the inter-operability of DNA design and simulation tools, user-friendly tools to improve oxDNA accessibility for non-expert users. I was invited as a contriubtor for brain-storm and presentation of the next-generation of software developments. I presented a talk about 'Numerical Study on the Effect of Flexibility in DNA Building Blocks'.


Other Researches

March 2018 to April 2018
Nanobiosensors Research Project, Begbroke Science Park, Oxford

Department of Continuing Education, University of Oxford, United Kingdom
Project title: 'Optical Transduction Mechanisms in DNA-based Nanobiosensors for Fluorescence Detection'
Supervisor: Dr Christiane Norenberg

June 2017 to Sep 2017
Summer Research Placement, the University of Cambridge (Cavendish Laboratory- Biological and Soft Systems group)

Department of Physics, University of Cambridge, United Kingdom
Project title: 'Automatic image analysis and extraction of cell cycle parameters in stem cells with FUCCI expression'
Supervisor: Prof. Pietro Cicuta

Sep 2015 to Sep 2016
Biomedical Research Final Year Project, the University of Nottingham

Department of Engineering, University of Nottingham, United Kingdom
Project title: 'Connection of wearable electronics to photonic textile'
Supervisor: Prof. Stephen Morgan

Jun 2015 to Aug 2015
Student Researcher, the University of Nottingham, United Kingdom Engineering Research Placements (ERPs) sponsored by the BP Company

Department of Engineering, University of Nottingham, United Kingdom
Research topic: ‘Effects of Nano-diamonds additives as anti-friction and anti-wear additives for automotive oils’
Supervisor: Dr. Antonino La Rocca

Honours and Rewards

Oct 2018 : Cambridge Trust Scholarship for Doctal of Philosophy in Physics.
Sep 2018 : Outstanding Graduates from the Department of Continue Education,University of Oxford.
Jul 2016 : Contribution to Undergraduate Studies Award to the top graduates in department.
Sep 2015 : Presented High Fliers Award to the top 5% of students in Faculty of Engineering.
Aug 2014 : Winner of an Industry Sponsored Scholarship in the University Research (£1,600).
Sep 2013 : Provost’s Scholarship for outstanding academic performance award to top 1.5% in division.
Sep 2012 : Head’s Scholarship for excellence academic performance award to top 5% in university.

Skills

Excellent PC programmer:
Skilled in C language, C++, Java, Objective Oriented Programming, Embedded Software Coding.
Keen user of algorithms method within Engineering Software Design.
Proficient user of R/Python/Perl/Pascal/Html Languages.

Interdisciplinary learner:
Electrical and electronical engineering (Control system design, digital and telecommunications, power networks and supply, electronic construction, signal processing, professional skills and mathematical techniques for electrical and electronics, VLSI design).
Computational biology (Genetics, statistics, neuroscience, genome informatics, function genomics, probability, population genetic analyses, structural and system biology).
Nanotechnology (Nanoscale-electronics, Nanotechnology for medical and health care, Nano-additives).

Hardware::
Digital IO and Processor Design, Microcontroller, Feedback and Control Systems, Signal Processing, Analogue and Digital Communication.
Software::
Photoshop, PSpice Schematics, Auto CAD, Matlab, Proficient user of emails, internets, commands and applications in Windows/MacOS/Unix/Linux systems.

Interests

Piano (Intermediate player), Tennis (2 years in university), Football and Badminton (5 years).
Sudoku, Rubik’s cube, Programing (Practiced from teenage). Travel around the world.

University Activities

-Winter Schoold Orgnizor for Department of Physics, Cavendish Laboratory, University of Cambridge.
-Executive committee member of Chinese Students & Scholars Association in Cambridge (CSSA), University of Cambridge.
-Team leader of Fundamental Science of Nanotechnology Assignment, University of Oxford.
-Student representative of the Engineering Department for the last three years; attended four Learning Community Forum Meetings (LCF) organized by the University of Nottingham.
-Completed the Summer Training Camp organized by the Department of Electrical and Electronic Engineering.
-Received Personal Service Recognition Certificate for volunteer work (University of Nottingham)
-Received outstanding student award for performance in Student Society Awards (University of Nottingham)