Biological Physics and Biophysics

Biological Physics at York

Biological Physics and Biophysics at York involves biophysics research and teaching which includes experimental and theoretical biophysics tools spanning multiple length and time scales, as well the use of physical science tools and techniques to address biophysics questions in the life sciences, physical methods of relevance to applications in biomedicine, and approaches which use biophysics in the context of biological-derived material to explore new physics. The Biophysics Group is an enthusiastic, growing team comprising multiple biophysics research groups spanning multiple research themes in the Physics Department at the University of York, and we interface closely with the University of York’s Biological Physical Sciences Institute (BPSI) and through a range of cross-departmental collaborations between physical and life scientists focused on a range of biophysics questions.  

Researchers

Andrew Gibson‌‌

Dr Andrew Gibson

Centre for Future Health Research Fellow

 

andrew.gibson@york.ac.uk

Interests

My research focusses on the development of computational approaches to study the interactions of low-temperature plasmas with cellular environments and drive their applications in biomedicine. These applications are motivated by the unique ability of low-temperature plasmas to produce high quantities of reactive oxygen and nitrogen species (RONS) at ambient temperature. RONS are crucial for an array of cellular functions, forming the basis of redox biology. As a result, plasma treatment of cells is capable of modifying their redox environment, inducing diverse biology responses ranging from cell death to proliferation. Currently, my work is exploring how computational approaches adapted from plasma modelling may be applied to study the complex redox chemistry involved in the plasma-cell interaction system. Overall, this research aims to develop a fundamental understanding of these interactions in order to accelerate low-temperature plasmas towards the clinic.

 

Robert Greenall

‌Dr Robert Greenall

Reader in Physics

robert.greenall@york.ac.uk

Interests

Research interests: The effects of polycations on the conformational properties of DNA have been investigated using classical molecular dynamics simulations. The current focus is on molecules that intercalate into DNA, such as ellipticine (a DNA topoisomerase inhibitor) and daunomycin (an anti-leukemia agent).

Teaching: The fourth year MPhys Molecular Biophysics course introduces physical concepts, models and experimental and theoretical techniques from the physical sciences that are used in the study of biological systems. It encompasses x-ray and neutron scattering to determine structure, the physical forces that stabilise structure and the thermodynamic and statistical mechanical basis of the dynamics of biological systems.

 

Yvette Hancock  

Dr Yvette Hancock

Lecturer in Physics

y.hancock1@york.ac.uk

Interests

Hancock's group employs interdisciplinary research at the physics-biological interface. Methods include quantitative Raman spectroscopy for biomarker determination in cancer, regenerative medicine, infectious disease, antimicrobials and bio-archaeology in collaboration with many key Departments (Biology, Computer Science, Chemistry, Mathematics, Electronics, Archaeology) and Centres (The Cancer Research Unit, Centre for Chronic Diseases and Disorders, BioArCh) at the University of York, in the UK and internationally. Her group aims to develop Raman spectroscopy biomarking for rapid disease diagnosis, understanding disease mechanisms and for treatment development. Her group also develops Raman analytical software and performs theoretical modelling of materials systems for nanoscale and biological applications. New collaborations are always welcome.

Dr José Juan-Colás

Centre for Future Health Fellow

 

jose.juancolas@york.ac.uk

 

Interests

My multidisciplinary research focuses on the development of novel biosensor technologies for healthcare, biomedical science and environmental monitoring [1,2,3,4]. Currently, I am developing new technologies to understand and control how diverse bacteria grow and form potent polymicrobial communities. Understanding the bacteria that make up these communities, how the community is structured and how bacteria interact with each other and with the host is critical if we are to slow the spread of antibiotic resistance, which has been named as a “crisis for the health and wealth of nations”.

Particularly, I am using microfluidic systems for bacterial co-culture in which the local growth conditions are regulated on-chip, while incorporating different non-destructive measurement techniques (such as on-chip Raman spectroscopy and label-free optical and electrochemical sensors) to study their evolution.

1. Nature Communications, 7:12769, doi:10.1038/ncomms12769
2. ACS Photonics, 2017, 4(9), 2320–2326, doi:10.1021/acsphotonics.7b00580
3. Sensors, 2017, 17(9), 2047, doi:10.3390/s17092047
4. Springer International Publishing AG, doi:10.1007/978-3-319-60501-2

Mark Leake‌Prof Mark Leake

Chair in Biological Physics

mark.leake@york.ac.uk

 

 

Interests

My work on bespoke microscope design and ultrasensitive imaging technologies has led to insight into how biological reactions progress in real time. Early work included optical tweezer instrumentation to probe mechanical properties of muscle (1), interferometric imaging approaches for the study of flagellar motors in action(2) and single molecule fluorescence imaging of membrane proteins in bacteria (3). I developed single molecule tools to dissect the architecture of bacterial DNA replication machinery resulting in the first observation of three DNA polymerases at replication forks instead of the historically accepted two(4). Development of these tools resulted in direct observation of the mechanisms of structural maintenance of chromosome (SMC) proteins, required for chromosome processing in all organisms (5). Current projects focus on single molecule fluorescence probing of DNA-protein machines in cells, biofilms and tissues, and new tools of magneto-optical tweezers with super-resolution imaging(6,7).

1. (2004) Biophys. J., 87, 1112; 2. (2005) Nature, 437, 916. 3. (2006) Nature, 443, 355; 4. (2010) Science, 328, 498; 5. (2012) Science, 338, 528; 6. (2015) Methods, 88, 81; 7. (2015) Photonics, 2, 758.

Tom McLeishProf Tom McLeish

Chair of Natural Philosophy

tom.mcleish@york.ac.uk

 

 

Interests

My research maintains a core of soft-matter and biological physics, especially concerning the role of random processes in protein dynamics, self-assembly of bio-molecular fibres and in evolution itself. 
I also have broad interdisciplinary research interests concerning science within wider historical and cultural contexts. These include collaborative work on medieval science, the philosophy of strong emergence, the entanglement of science with literature and the theology of science.

Projects include:

Dynamic mechanisms of Protein Allostery

  • Self-assembly of Silk Fibres under Flow
  • Statistical Mechanics of Evolution
  • Interdisciplinary Readings of the Scientific Works of Robert Grosseteste
  • Wisdom Literature and a Theology of Science
  • Comparative Creativity in Arts, Humanities and Sciences

Dr Agnes Noy

EPSRC Advanced Research Fellow

agnes.noy@york.ac.uk

Interests

I am an EPSRC Fellow with a multi-disciplinary trajectory in molecular modelling between biochemistry and biophysics. My research interests have been centred in developing novel computational tools to understand and predict how global mechanical properties of complex macromolecules such as DNA and RNA are built on the basis of their atomic fluctuations, with a particular emphasis in DNA flexibility and supercoiling. My research group will focus on understanding and predicting the 3D architecture of bacteria genomes on a broad range of length scales with a multi-scale approach: from atomistic and coarse-grained simulations to statistical-mechanics algorithms.For more information visit www.agnesnoy.cat

Nature Methods, (2016), 13, 55; J Chem Theor Comput, (2015), 11, 2768; Phys Rev Lett, (2012), 109, 228101.

Deborah O'Connell‌Dr Deborah O’Connell

Reader in Physics

deborah.oconnell@york.ac.uk

 

Interests

The aim of my research is to understand and develop low-temperature plasmas for tailored applications, including emerging biomedical technologies. Low-temperature plasmas or ‘cold’ plasmas exploit the fact that they are effective and tuneable sources of reactive oxygen and nitrogenspecies (RONS), known to play an important role in biological systems. These plasmas have been demonstrated as having potential in for example anti-cancer treatments, antimicrobials, and wound healing. My research group is inter-disciplinary and we collaborate closely with research groups across the Departments of Biology and Chemistry.

 Chem. Eur. J. (2016) 22, 3496;  Tumor Biology (2016) 37 6 7021; British Journal of Cancer (2015) 112 1536

Dr Stephen Quinn

Dr Steven Quinn

Lecturer in Biophysics

steve.quinn@york.ac.uk

 

Interests

I am a Lecturer in Biophysics, specializing in multidisciplinary science across the Departments of Physics and Biology. My work combines recent advances in biochemistry with state-of-the-art microscopy tools to probe the molecular building blocks of human life and disease. My focus is the application of single-molecule microscopy techniques to investigate complex biological processes in order to drive the rational design of next-generation therapeutics. 

The field of single-molecule biophysics is at the forefront of the life-sciences interface, allowing the very building blocks of human life (DNA, RNA, proteins) to be explored with unprecedented levels of detail. By following individual biomolecules at work, we can directly measure biological interactions, chemical reactions and discrete structural changes that may be impossible to detect by conventional methods. Single-molecule techniques are uniquely placed to enable us to understand how biomolecules and molecular machines function. 

My early work led to the development of new approaches for monitoring protein-protein interactions heavily linked with Alzheimer’s disease (Mol. Biosyst. 2014, 10, 34-44) and for the screening of inhibitors (Mol. Cell. Neurosci. 2014, 61, 46-55; ChemBioChem 2016, 17, 1029-1037). I have also investigated how DNA base-pairing is modulated by molecular crowders (J. Am. Chem. Soc. 2015, 137, 16020-16023), developed a platform for identifying carbohydrate interactions (ChemPhysChem. 2016, 120, 19487-19491) and created a sensing technique based on quantum dot light emission for identifying toxic MRI contrast agents (J. Phys. Chem. C. 2016, 120, 19487-19491; RSC Adv. 2017, 7, 24730-24735).

We are currently targeting protein-protein interactions related to cancer and protein-induced disruption of lipid membranes and their link to neurodegeneration. The primary experimental approaches combine advanced fluorescence microscopy tools, such as total-internal reflection fluorescence (TIRF) imaging, with cutting-edge biophysical and biochemical techniques.

Laurence Wilson‌Dr Laurence Wilson

Lecturer in Biological Physics

laurence.wilson@york.ac.uk

 

Interests

Our group in the physics department at the University of York specialises in the application of novel optical microscopy techniques. In particular, we take advantage of high-speed imaging and advanced image-processing algorithms, coupled with classical optics principles and scattering theory.  We have recently used approaches based on dynamic light scattering and holography to give new insight into the swimming behaviour of micro-organisms including E. coliC. reinhardtii, and cellular parasites such as Plasmodium and Leishmania.   Our group website contains more details about our techniques and publications.

Nat. Commun. 6 7985 (2015).; Proc. Natl. Acad. Sci. USA 110(47) 18769-18774 (2013).;  Phys. Rev. Lett. 106 018101 (2011).

Adam WoolmanDr Adam Wollman

Centre for Future Health Research Fellow

adam.wollman@york.ac.uk

Interests

Glucose fuels the human body and if not regulated correctly, as in diabetes, causes serious health problems. Over 400 million people have diabetes and it is now one of the leading causes of death worldwide. My research has tried to understand these basic mechanisms using yeast cells as a model organism and imaging them with a novel fluorescence microscope, which I designed and built, and is capable of imaging the individual protein molecules that sense and respond to glucose.

To better understand glucose metabolism, I propose to develop a new glucose nanosensor which can enter the cell and measure, for the first time, the amount of glucose taken up by a living cell. This sensor technology could also have a more direct clinical application as the greater sensitivity would allow glucose monitoring from saliva, sweat or tears rather than the current more invasive blood sampling that is required.

I have designed and built a single molecule microscope at the University of York and applied it to many life and health science problems. Mentored by Prof. Mark Leake and working with many excellent collaborators, I have investigated transcription factors in yeast (eLifeFaraday DiscussionsFEMS letters), DNA replication in E.coli (eLife), division in S. Aureus (Physical Biology), human immune cells and toxins (bioArXiv) and more.

For microscopists, I utilise many super resolution and other techniques including: Slimfield, TIRF, FRAP, PALM, STORM, confocal, EM, Optical and magnetic tweezers.

The Biophysics Group was established in 2015 following a series of open biophysics discussion events, where it became clear there were significant emergent activities aligned either directly with addressing biological questions, or with applying biophysics to applications in the life sciences, including the use of biological or bio-inspired devices and materials.

The resulting Biophysics and Biological Physics seminar series is a networking vehicle running 4-6 times each term. The rising attendance of now 20-30 people stimulates lively discussions, allows junior members to find their voice and provides focused project talks as well as talks from biophysics experts from other departments.

We actively encourage new interest in the Biophysics Group, and are delighted to discuss possibilities of new recruitment in to biological physics and biophysics. Just drop us an email and we will explore the ways in which we can help you develop your ideas.

Upcoming biological physics seminars

  • Ji-Eun Lee — 16:00, 22 June 2018 (B/B/103)
    Characterization of Nano-Objects using Single-Molecule Fluorescence Microscopy

Twitter updates

Biological Physical Sciences Institute (BPSI)

Biophysics Away Day, Sandburn Hall, March 2018

Biological Physics Away Day, Sandburn Hall, March 2018