Below is a list of DPhil projects for 2022 in biological physics; please address all informal enquiries to the named supervisor.

Biological rotary molecular motors

Richard Berry

Nature DID invent the wheel, at least 3 times! The bacterial flagellar motor is 50 nanometres across, spins at over 100,000 rp. driven by electric current, and propels swimming bacterial cells. ATP-synthase is even smaller, about 10 nm across, consists of two rotary motors coupled back-to-back, and generates most of the ATP – life's 'energy currency – in most living organisms. We are trying to discover how these living machines work. We develop and use a range of methods in light microscopy including ultra-fast particle tracking, magnetic and optical tweezers and single-molecule fluorescence microscopy. Current projects in the lab: measurement of stepping rotation and mechano-sensing in flagellar motors, synthetic biology using ATP-synthase,single-molecule fluorescence microscopy of protein dynamics in bacterial motility and chemotaxis, high-torque magnetic tweezers, templated assembly of flagellar rotors using DNA nanotechnology scaffolds (collaboration with Turberfield group). More information can be found here.

Nanoscale imaging of molecular machines working on DNA

Achillefs Kapanidis

As Richard Feynman noted back in 1959, 'it is very easy to answer many of these fundamental biological questions…you just look at the thing!' Our research group is turning this bold vision into a reality by developing and applying cutting-edge methods to monitor sub-nanometre motions of single molecular machines with sub-millisecond temporal resolution. Our work focuses on the mechanisms of the protein RNA polymerase, which copies DNA into RNA during the process of gene transcription. This protein is a major target for antibiotics, making our work important for understanding and controlling antibiotic resistance of bacteria, one of the most pressing health challenges the world faces today.

Available projects focus on watching the nanoscale dynamics of RNA polymerase in real-time to find new steps and paths in transcription, and on understanding how antibiotics control nanoscale motions of RNA polymerase to control the spread of pathogenic bacteria. These efforts rely on our ability to detect single molecules of RNA polymerase as they copy DNA fragments that resemble expressed genes.

Projects will involve single-molecule imaging, measurements of 1-10 nm distances within protein-DNA complexes based on dipole-dipole interactions between dyes attached to specific sites (via the method of single-molecule FRET), molecular modeling, quantitative modeling of reaction kinetics, and advanced signal processing of large data sets.

For a recent example of our work:
Duchi, Bauer… Kapanidis, Molecular Cell 2016, 63, 939-950
Dulin, Bauer… Kapanidis, Nature Communications 2018, 9, article number: 1478

Super-resolution imaging of DNA repair and gene expression in living cells

Achillefs Kapanidis

A new type of optical microscopy is currently revolutionising biology and medicine. Super-resolution imaging, as it is known, relies on ingenious ways that circumvent the resolution limit imposed by the diffraction of light; the potential of these methods was recognized by the award of the 2014 Nobel Prize in Chemistry to three physicists. A popular super-resolution method relies on detecting single fluorescent molecules, and is known as single-molecule localisation microscopy. Localisation microscopy bypasses the diffraction limit by finding the location of a fluorescent probe with a precision of up to 100-fold better than the width of its point-spread function (PSF; see figure). Provided that sufficient photons are collected, we can localize single fluorescent dyes with ~1 nm precision, 250-times better than the optical resolution limit.

We offer projects on three main areas in super-resolution imaging. First, the development of new ways to break the diffraction limit either for immobile or diffusing molecules. Second, the adaptation of existing methods to study the 3-D organisation, diffusion, and mechanisms of protein machines in single cells; we are interested in how DNA-binding proteins combine 1-D and 3-D diffusion to find their targets (a difficult problem: finding ~20 letters within 4,500,000 letters of chromosomal DNA), how cells repair their DNA rapidly and incredibly accurately, and how bacteria modulate their gene expression in a noisy environment. Third, the development of quantitative and stochastic mathematical models to describe the DNA-related processes we study.

For a recent example of our work: Stracy,… Kapanidis, PNAS 2015, 112, 4390-4399

Ion channels and nanopores: from structure to function

Stephen Tucker

Almost every single process in the human body is controlled at some level by electrical signals, from the way our hearts beat, the way our muscles move, to the way we think. These electrical signals are generated and controlled by a family of proteins called 'ion channels' which reside in the membrane of every living cell and which act as 'electrical switches' to control the selective movement of charged ions like potassium (K+) and Sodium (Na+) into and out of the cell.

Work in our lab uses a range of multidisciplinary approaches (molecular biology, electrophysiology, single-molecule fluorescence, molecular dynamics and crystallography) to study the structure and function of these channels. We have a range of projects available to people with physics, engineering, computing, biochemistry and physiology backgrounds.

In particular, we currently have an exciting new DPhil project available to investigate how the unusual behaviour of water within the nano-sized pore of an ion channel influences its behaviour. This project would suit someone with a computational background and/or programming skills as it involves development of a new software tool to annotate membrane protein structures.

In collaboration with other colleagues in Oxford, we also have PhD projects available to work on the structural determination of ion channel drug binding sites using serial femtosecond crystallography and X-ray free electron laser (XFEL).

Self-assembled structures and devices

Andrew Turberfield

We are exploring applications of biomolecular nanofabrication at the interface between the physical and life sciences. DPhil projects are potentially available in any of the areas outlined below. We come from a wide range of scientific backgrounds, including physics, chemistry, biochemistry / molecular biology, engineering and computer science, and apply tools and techniques from these disciplines to important problems in science and technology. In 2021 we will be moving to a new interdisciplinary research centre, just across the road from our current home in the Clarendon Laboratory, which will greatly enhance our ability to undertake collaborative projects with colleagues in the biomedical sciences.

We create nanostructures from biopolymers – especially DNA and, increasingly, RNA. We control assembly by designing the base sequences of short, synthetic, strands of DNA to control their interactions. Programmed self-assembly enables rapid and flexible construction with near-atomic precision: designs can be developed in days and structures (sometimes!) made in minutes.

  • Our work on synthetic molecular machinery includes molecular motors, a ‘synthetic ribosome’ (genetically-programmed molecular machinery capable of sequence-controlled synthesis of non-biological polymers), and molecular robotic devices that combine autonomous sensing, computation, and actuation. Some of the most exciting potential applications of molecular robots are in medicine: we are also developing 'theranostic' devices, integrated systems that are capable of therapeutic intervention with single-cell resolution.
  • We are developing nanostructures as intracellular sensors and markers, for ultra-high-resolution structural measurements by cryo-electron tomography.
  • We study nanostructure folding, with the aim of understanding and designing assembly pathways in order to enable efficient construction. Particularly interesting, and challenging, is the creation of a nanostructure from a single strand of RNA as it is generated (transcribed) in vitro or in a cell.
  • We use the nanometre-scale architectural control provided by DNA assembly to study the interactions between peptides (with the Woolfson group, Bristol Chemistry) and the assembly of protein components to make large molecular machines such as the bacterial flagellar motor (with the Berry group, Department of Physics).
  • We are using DNA templates to organise molecular components into circuits to create and study molecular electronic devices (with the Ardavan group, Department of Physics).

Examples of publications from our wide range of interdisciplinary projects:
Peptide Assembly Directed and Quantified Using Megadalton DNA Nanostructures. J. Jin et al., ACS Nano 13, 9927-9935 (2019)
The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery. R. K. O’Reilly et al., Acc. Chem. Res. 50, 2496-2509 (2017)
An Autonomous Molecular Assembler for Programmable Chemical Synthesis. W. Meng et al.,Nature Chem.8, 542–548 (2016)
Guiding the folding pathway of DNA origami. K. E. Dunn, F. Dannenberg, T. E. Ouldridge et al.,Nature 525, 82–86 (2015)
Direct observation of stepwise movement of a synthetic molecular transporter. S. F. J. Wickham et al., Nature Nanotechnol. 6, 166-169 (2011)