剑桥大学 物理学博士

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

剑桥大学-卡文迪许实验室,Department of Physics, University of Cambridge, United Kingdom

博士论文链接:View my PhD Thesis

剑桥大学 生物计算-应用数学系硕士

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

Department of Applied Mathematics, University of Cambridge, United Kingdom

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牛津大学 纳米医学研究生

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

Department of Continuing Education, University of Oxford, United Kingdom

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诺丁汉大学 电气工程及自动化本科

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

Department of Engineering, University of Nottingham, United Kingdom

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研究项目

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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发表文献:

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)

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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'.


其他研究

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

荣誉和奖项

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.

专业技能

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.

兴趣爱好

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

社团活动

-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)